Color Notes:
Black: Just commenting/don't see as much of an issue.
Red: Can be left behind, possibly may not want back.
Yellow: Doesn't have to be in every gen but like for it to come back once in a while.
Blue: Would like to come back but willing to compromise.
Green: Should be a feature in every gen.
Masuda's Quotes: For the two above the title I don't really have anything to say about them. GF not distinguishing between "experiments" and "features to keep" makes sense in a way as they don't know how fans would react to a certain feature, essentially they make a batch of features and throwing them out there to see what sticks. And while you can argue about all the liked features that were cut, they have indeed kept plenty of features too. However I feel one problem in this regard is that, when they decide to drop a features, it feels like a permanent decision (until they do a remake) and they don't really go back on the decision. Just like with them not doing a Fossil Pokemon or Eeveelution every generation, may not be a bad idea to give a certain feature a rest but then go back to it after a generation in the oven to do new ideas with (it may have also been an idea thought up "too early" and back when it wa introduced the technology just wasn't there to fully bring out its potential).
Smartphones: As for the bottom quote, you know what GF, if you REALLY feel that Smartphones and Tablets are providing a wider experience than why not turn some of these older features into a Smartphone app we connect with the games? Contests, Secret Bases, The Underground/Join Avenue/WiFi Plaza, PokeStar Studios, DREAM WORLD, Pokeathlon, Game Corner, Poke Pelago, Battle Frontier, even Pokemon-Amie/Refresh/Camp. Any of these made into their own app would have millions of downloads and if GF make them updateable when a new gen comes out they can "keep them" as a staying feature (whether they update it at launch or later which they can advertise as a "coming soon feature" sort of thing).
National Dex: With Dexit this is really no longer an issue. And, once again, I'd like to state that I have no problem with Dexit, it was something I think was coming even if they could bring all the Pokemon over. If I had displayed any issue with Dexit was because of their reason to do it, I always thought a reason to do a Dexit was so they could really focus on the included Pokemon and make them the best they possibly could which would include stat updates (if not completely redoing their stats), entire movepool & level-up update, seeing if they could give them better Abilities or updating Abilities to make them better, possibly improving Signature Moves or making new Moves to fill gaps, etc.. However advertising it's for better graphics while showing low-res graphics (though I heard that's just for the Wild Area and everywhere else the game looks beautiful... though advertising is everything and they REALLY pushed the Wild Area so not that great of a first impression) and then having the Dynamax mechanic (which, if you think about it, would mean there's probably just as many Pokemon models in the game as there would have normally been) made the decision to do so feel hollow for THIS generation. Of course they could have updated every Pokemon included and not just advertised it (fat chance, though they at least did put in new mechanics that'll help making a competitive team more easier, though that's something they could have easily done without Dexit). So, overall, I don't think them no longer having a National Dex is that big a deal, though I would like them to reconsider not having patches that would add in more Pokemon.
Following Pokemon: I'm iffy on this one. I would like it but I can see it being problematic for some Pokemon. I'd be more willing to compromise on this one: reasonably sized Pokemon I think should be allowed but large Pokemon, sorry buds, but we're exploring places usually made for human sized creatures.
Riding Pokemon: Another I feel iffy about simply because on land I prefer using the Bike. Sure the Poke Rides gave us additional abilities depending on the Poke Ride and LGPE had some fun/amusing Pokemon you rode on, but I don't think it would be such a crime if they aren't brought back every generation. Only acceptation I would say would be for surfing, unless that generation made an alternative surfing method (like Galar using a Water Bike) I wouldn't mind if they gave you an option of what Pokemon you want to ride on to get across water.
DexNax/Habitat List: This should be in every game. It makes actually filling the dex feel more fulfilling if not easier as you're not just trying to fill out this blank spot in a massive list but actually listing all the Pokemon that live in this location. And since it's separated into smaller groupings you could provide rewards for completing them or have features that let's you catch a better/special/unique Pokemon in that location (better IVs, knows a special Move, has Hidden Ability, is Shiny, etc.).
Player Search System: I think this is a good example of what the general communication feature between players should be like. Gen VII's Festival Plaza felt too intrusive, requiring you to actually "leave" the game to enter this area to communicate with other players. Thankfully Gen VIII's Y-Comm looks to be taking notes from the Player Search System so I wouldn't say this is much of an issue (at least for this gen).
Super Training: Eh, Super Training was fun but felt like there were easier ways to EV train. Like during the main game, sure it's the best way to get your Pokemon to high/max EVs, but post game feel other options open up (like Vitamins) that makes Super Training feel less convenient. Poke Pelago and now Poke Jobs offering quick, easy, and working in the background to get EVs I feel is the way to go as you would still use those features even in the post game.
Soaring: Was fun and would like back if the context is there for it. I say maybe make it something for the remakes, giving us a new way to look at a region we thought we knew.
Contests: I always felt them removing Contests was a mistake. Out of all the "side features" (Contests, Pokeathlon, Musicals, & PokeStar Studios) I fee like Contests did the best showing Pokemon were more than just battling. And Contests had deep mechanics and strategy to it, if you really want those Master Ribbons you had to know what you're doing and specifically prepared your Pokemon to win. Pokeathlon, Musicals, and PokeStar Studios were fun distractions that gave you all that you wanted from it, but Contests I feel had the potential to be a strong mainstay especially if they worked on making ways to give it ease to access (it may even lead to innovations to the battling side of things).
Safari Zone/Friend Safari: Honestly, as long as they provide us interesting locations to catch Pokemon in, I don't mind if they don't have the Safari Zone if they don't feel it's needed. If they ever do a Safari Zone I would like it on the level as HGSS's Safari Zone where it's customizable. As for the Friend Safari, neat idea though I feel it's limited and made some player's Friend Safari better than others (and each one obsolete as soon as you caught the Pokemon you wanted). Think a better way of doing the Friend Safari, maybe even having it connect to the normal Safari Zone, would be for each player you have on a friend list randomly adds an additional Pokemon to the Safari Zone and changes each day. That way some players aren't better than another, they don't become obsolete after catching the Pokemon they provide (as it would be random), and you're not locked out from getting a certain Pokemon because you aren't friends with the right person and actively encourages to register as many players as you can.
Ball Seals: Now Pokemon is getting better as player customization but I think there's still more it can do. I can tell you all the things I would like to see done other games are doing when it comes to the player's appearance, however that's just for the player's avatar. What about the Pokemon? Now you can't dress the Pokemon up because that'll probably make the programmers have a nervous breakdown (so them bringing back Pokemon Musicals for the BW remakes should be a "fun time" in the GF offices). However Ball Seals I think is one way to let the players customize their Pokemon in various ways. I'd say let us even customize the Poke Ball itself by choosing its colors with us having to work within the pattern of the Poke Ball (also giving us a way to switch a Pokemon into a different Poke Ball would be nice too). GF has just made a major leap forward in letting us customize our Pokemon's battling traits, this would be an easy way of letting us customize a visual directly connected to the Pokemon.
Battle Frontier/Inverse Battles: I would love a Battle Frontier, or if we can't have that a separate Battle Revolution game (or an app as I suggested above). However I can also understand creating multiple different Battle Facilities for a part of the game which many players may not play doesn't sound that enticing. However that doesn't mean they should completely throw out all those interesting ways to change how battles work. Each game has a Battle Tower expy but the modes within it is always just the plain ol' Single, Doubles, and maybe another battling style that's an extension on the normal way of battling. Why not make special modes within the Battle Tower expy that is based on what would be a Battle Facility gimmick? A mode to do Inverse Battles, a mode to do Little Cup, a mode to do Rentals, and etc.. They could even use this as the design basis for the Battle Tower expy, making it a location which would have such a diverse array of styles like maybe a television studio, a giant castle, a massive underground dungeon, etc.. Another suggestion is connecting a Battle Facility with a location that would normally be in the game like the Trainer School or the unique battling location (White Treehollow, Black Tower, Battle Royale).
World Tournament: Eh, ambitious and, while it or an expy would be welcomed again, it is something where you DON'T want it every generation. Now certainly they can bring back popular trainers for cameos and have them battleable in locations like the Battle Tower expy. However for something where it brings ALL (well, MOST) of the important trainers from the previous gens together, that's something special that should be saved for special occasions. Gen V was a good time to do it as Pokemon had passed its 10th year anniversary and Gen V was the start of the games being based on locations outside of Japan so gave a sense of a bigger world that's all connected. I feel the next milestone for a World Tournament-like competition would be Gen X/10. One reason is because of Dexit, if GF is gonna keep to this Limited Dex idea I feel they need both this and Gen 9 to work out how they'll do it (how it'll affect other versions within that same generation, maybe allow patching in Pokemon) before they plan a big battle tourney where they'd bring back all these older NPCs who you'd want to see using their signature Pokemon thus those Pokemon would need to be part of the regional dex.
Roaming Legendaries:
... If they must bring back this mechanic at least make it like XY where it's more that you're tracking down the Pokemon until it goes back to its lair.
Difficulty Modes: B2W2 poorly implemented them (especially by locking them until you complete the game, WTF). But if from the Option menu you could choose to have battles with trainers be more easier or difficult I think that would be good. Now how many layers of difficulty and how it'll change the battles is another question and debate entirely, but for a start let's just at least have them.
Mega Evolution/Z-Moves/Dynamaxing: Yes, I'm including Dynamaxing pre-preemptively as they announced it wasn't lasting into Gen 9. My main concern are with preserving the designs. We have many Pokemon with "super forms", and it's my personal belief that if those Pokemon are in the game they should have access to that "super form". BUT, I don't think it should be just limited to the mechanic in which that super form debut in. No reason to re-invent the design of the wheel if the design is perfectly good. Heck, I'm not against re-adjusting the designs so they could fit into the new "equalizer" mechanic's aesthetic (though if aesthetic is drastically requiring you to change or make compromises to designs I ask if there isn't a problem with the aesthetic and shouldn't be changed or abandoned... like Pokemon growing huge, probably could have decreased the size grown or just not do it cause aside from SOME Gigantamax it's not that visually impressive).
Similar with Z-Moves and Max Moves, now that we got them do we really need to ever do a "super move" for each Type again? If you want a powerful looking super move re-use the Z-Moves (even if you don't call them Z-Moves), if you need an impressive looking move that does a useful effect re-use the Max Moves (even if you don't call them Max Moves). That way you can then focus on making more unique super moves.
Secret Bases/Join Avenue/Festival Plaza: I feel it was a missed opportunity having Secret Bases expies. While I liked the Secret Bases, I felt like they were TOO secret. Because if you're going to customize a room you're going to want other players to see it yet the requirement to have players see your Secret Bases always felt out of the way to do to be worth it. In Hoenn there was only a limited amount of Secret Bases that could be made and for some you had to go out of the way to get to. In Sinnoh they were part of the Underground meaning they all were just holes in the wall and only really existed if you played the flag catching game. I don't want them to just bring back Secret Bases, I want them to make Secret Bases expies where its easier to show off this personal space you made.
This is where Join Avenue and Festival Plaza come in. I feel like what they did with those is maybe what they should do with the Secret Bases. While you'll certainly have your own space to fill with furniture & decorations I also feel there should be things which benefits other players taking time to visit your personal space. Like one idea is that maybe have a town, maybe even your hometown, that you can help buildup, invite people to move to, and decorate (like in Animal Crossing, specifically New Leaf). Or maybe give us a space to actually make our own Gym and we can decide what it looks life, puzzle pieces to include, invite trainers to be in it, and have like a gift shop room which provides items and services for anyone visiting it. A lot of cool potential, maybe even some they can link into the game's theme.
WiFi Plaza: Eh, like having an amusement park place where you and other players can join up and play mini-games is a fun idea but I feel the above Secret Bases, Join Avenue, Festival Plaza has it beat. If they want players able to compete in mini-games wait for my comment on Game Corner.
PokeStar Studioes: I feel this is one of those mechanics they can put away for a bit and then bring back every once in a while, let the technology advance a bit as with movies the spectacle is the main attraction so the more you can do with the visuals the more interesting things you can do with the movies.
Mach/Acro Bikes: I thought we solved this problem in Gen IV? Combine them together, heck why did they separate them for ORAS? SwSh looks like it's going to take the idea of the bike even further so this point moot.
O-Powers/Roto Loto Power: Sure, having these passive power-ups are nice and gives you a neat thing to gift other players when you connect to them. Has it been confirmed the Y-Comm has a similar feature?
Swarms: Were certainly fun but not an absolute necessity, I think players liked chaining more anyway. I also personally preferred the Island Scan mechanic, maybe they could combine the two together.
Horde Battles: Neat idea but I felt it fell short and not worth improving. Rather they have Wild Double Battles and even SOS Battles.
Sky Battles: On paper sounded good... but I'm surprised it actually made it into the game once they saw how limited it was.
Seasons: Seasons not only add visual appeal but can be used to help make more Pokemon available in a certain area and also expand upon exploration. Obviously certain Pokemon would be adapted to certain seasons so depending on the season a Pokemon may be more available, less available, or not available (may also give earlier access to certain Types like Ice and Fire). As for exploration the different seasons can change the environment so that it both opens and closes pathways & entrances. Winter could have snow piles block places but also able to be climbed to access higher places otherwise cutoff; Summer could dry out smaller water sources/lower water levels making surfing less useful but revealing hidden paths/caves; Spring could have vines grow that prevent access to a pathway but can climb up; Autumn has bushes lose their leaves revealing paths between them but all the leaves block up water sources causing waterways to be unusable. And these are just some examples off the top of my head.
PokeGear: Every gen we get a new Tool so don't see why the PokeGear alone gets a lone shout out (personally I would have focused on the Poketch as it was far more versatile, or the improvements they did with the ORAS PokeNav). Y-Comm is our new Tool for SwSh so let's see what it does before lamenting the loss of other Tools. Though would be neat if they had a Tool which just combined all the features past Tools have done.
Mom's Bank: ... was that such a major feature? Honestly the only reason to have a Bank of any sort was if there was a background way to earn money and that money instead went into a Bank instead of instantly to you. But otherwise no need for it.
Dream World & Pokemon Global Link: Let's see what Pokemon HOME does first. I would like HOME to have taken pieces of the Dream World & Global Link, at the very least so we can do stuff with the Pokemon waiting inside it.
Auto-Run Toggle: Okay you're now just looking for reasons to complain. WE RUN BY DEFAULT NOW! Actually, no, since we're now using an analog stick we can also sneak and walk if we wanted to, though 99% of the time you're going full tilt to run.
Second Region: *LOUD GROAN* ... there was a very good reason why Johto let you visit Kanto: THERE WERE RIGHT NEXT TO EACH OTHER! We have yet had another pair of regions which were next to each other. Only way I can see us getting a dual region game again is if the game's story was that it took place in two regions that were next to each other so they'd both be new regions. However I don't think we'll ever see a new region that goes "surprise! You can now visit this old region!"; especially with the way the Pokemon games are now jumping all over the world.
Pokeathlon: Like PokeStar Studios above, this can be a feature they bring back once in a while. Let technology and visuals advance.
Game Corner (As We Know It): So this one is a complex issue. The Game Corner as we know it, essentially a casino with gambling games, is forever dead.
Game Corner (But As An Arcade): HOWEVER that doesn't mean they can't bring back the Game Corner as an arcade where you play mini-games. Maybe even let you use some of your money so that you can earn BP ("Bonus Points") from the mini-games you can use to buy prizes. However, with that said, it's not a vital feature, just something fun to see come back every now and again.
Battle Tent: Battle Tents only existed because the Battle Frontier was a new mechanic and they wanted to give players a taste of it before it actually became available. No that the Battle Frontier is a well known feature they no longer have a purpose thus don't need to come back.
Berry Growing & Blending: I added Berry growing because THAT'S the main mechanic we should be focusing on. Yes, let us grow Berries, even if we're only allowed to do so in one location.
As for Blending... well I do think Contests should come back so obviously Berries would be used to make the treat that raises Contest conditions, though doesn't need to be blending. Heck, blending was only in RSE, in Sinnoh it was simply making Poffins by mixing the batter and ORAS got rid of the mini-game altogether (making it work like the Apriblender did with Apricorns to increase the Pokeathlon stats). So if they did bring back Contests for a new region not only would it have a new kind of treat but will probably have a different way of making it that may not even involve a mini-game.
Triple Battles/Rotation Battles: I say we bring them back. I'm pretty sure the Switch can handle six Pokemon on screen at once. It'll also give the Battle Tower expy some more "basic" battle modes.
Mythical Events: Not only would I want that back, but I think all Legendaries in that game's dex should maybe have an additional side event or two. They're supposed to be super special Pokemon yet once you catch them they might as well be a com mon as far as the game is concerned. Having some side event stuff you can open up with them will make these Pokemon feel special. Would be nice lore and maybe world building.
Trick House/White Treehollow/Black Tower: I included the White Treehollow and Black Tower because honestly I feel those are the ones we should be wanting back. Sure, Trick House is fun and has a lot of potential, but it was a side distraction at best. White Treehollow and Black Tower on the other hand was a location you could can fast experience points and money while testing your battling and strategy skills. Of course they wouldn't come back as White Treehollow or Black Tower, they would come back as an expy location. This is also why I combined them with Trick House as I can see they could combine the two together. Even if they kept the location post game I think any game would benefit having a location like them.
Vs Seeker/PokeNav Trainer Eyes: While I wouldn't make it work like the Vs Seeker, rather it worked like the PokeNav's Trainer Eyes, yes. I would like to have rematches against trainers I previously fought, especially the more notable and important ones. The Gym Leader rematches in the Battle Maison in XY didn't feel fulfilling as they only used two or three Pokemon, and rematches with important trainers in Gen VII was a major pain as you had to figure out where they appeared (mainly Title Defense or Battle Tree) and some were version exclusive! I want rematches like the ones Platinum or HGSS, there's a place you can go where the Gym Leaders and other important NPCs gather and you can challenge them and they'll have an entire team of stronger Pokemon.