I wouldn't be surprised if they pull the good ol' "My wish is the cure for a loved one's unspecified terminal illness" routine
I'll bet (for kudos points): The player's wish will be returning the Infinity Energy that was siphoned from the planet by Quasartico which started to cause harm to the environment (maybe even summoned the "A" Pokemon which is bad), thus why Zygarde is here.
Alternatively, if we stick to the "A" Pokemon being summoned idea, the wish could be used to Mega Evolve Zygarde (which would have the side effect of returning the siphoned Infinite Energy; so same result but with this one Zygarde gets a cool power-up at least).
EDIT:
Hugin beat me to it.
Emma is called Matire in Japanese, she'll be in M rank not E.
Diantha is called Carne in Japanese.
Just out of curiosity, everyone is joking right? Like we all know just because the "Z" and "Y" rank boss trainer has names that start with those letters it's likely not going to persist for the higher ranks if we want to see notable NPCs as Rank Bosses.
Or who knows, maybe all the "Rank Bosses" will be these "no names" while notable trainers will have their big battle with the player outside of that; keep story and Ranking Up separate. That way the notable NPCs can both not have their teams made restrictive and return for other battles later while the Rank Bosses will be one-and-done.
Though, with that said, now I wonder if we'll see any "team themes" done by the Rank Bosses. Like, I guess for 18 of them they can just do the Types... but that would be boring. This would be an opportune time to do unique team themes without worrying about them being a returning character like a Gym Leader or Elite Four member. OOH, I have an idea! Base their teams on the words of the
Unown Report! Like "ZOOM" fits with the Cab Driver pretty well and he'll use a team of fast Pokemon. Though all we know about Y Rank Boss is she wants her wish to create a city size marathon, Unown Y is "YIELD" which I'm not sure how that would fit (maybe she's hoping to yield attention & resources to a certain cause she supports?).
5) Trace works differently in ZA.
Would be nice if Trace was more selective what Abilities it would copy.
Mega Alakazam: "Now I'll use Trace to copy your... Synchronize? You know what you can keep that for yourself, I'll wait for the next Pokemon to see if their Ability is worth my time"
THAT said, I also discovered a possible 6th reason Trace didn't activate. The Pokemon that Alakazam is battling is a Gardevoir... a Pokemon that can also have Trace.

Is hiding whether they included Abilities really that big of a deal to them?
there's a certain pokemon whose name also goes from Z to A
(Zebstrika)
Hey, why leave out Pokemon who's name starts with "Za"? That'll give us Zarude who could use a bit more to its lore (also Zacian and Zamazanta, but I don't think they would be appearing... then again, I wouldn't have thought the Forces of Nature would be in Legends: Arceus but not only did they but got a new member so

. Would be funny if they update Behemoth Blade/Bash to also do double damage against Mega Pokemon).
And before someone says it, Zangoose and Zorua are already in the Kalos Dex so they don't count.
"To make it easier for people and pokemon to coexist, a company named Quasartico, Inc is carrying out an urban redevelopment plan."
That plan:
What am I supposed to be seeing?
Again, Paris Catacombs. They've got to do it.
Also opera house (or maybe in Lumiose's case one of the fancy restaurants like Sushi High Roller (they could then include an NPC that mentions the restaurant opening up new chains all over the globe, specifically namedropping Paldea... I bet no one realized there were Sushi High Rollers in Paldea, did anyone? Don't worry, neither did I until just now

).
Huh, random thought. Do we think the wish going to be something purely story-based(Wish for Zygarde to stop rampaging or the evil team to disband, a simple "advance the storyline to the conclusion" button), or is it going to have in-game ramifications? I could see your "wish" being a preset list of like 10 things, possibly even swappable by doing a "title defense" match or similar, where you the player choose "More high-level spawns in Wild areas" vs "More low-level spawns in wild areas" vs "better shiny rates" vs "2x rewards from battles" vs etc. You could flavor that as the company/govt using their resources to accomplish it fairly easily, and that would let the player focus the post-game on what they want.
Also, clothing customization is confirmed(check the minimap). I wasn't expecting it to leave, but with Gamefreak you never know.
Hm, while I'm of course going to go with my speculation, I could maybe see a post game thing where Quasartico (while they are the ones who would be siphoning the Infinity Energy, I'm gonna say they aren't doing it our of maliciousness but rather blind ambition to a seemingly infinite energy resource) will restructure the Z-A Royale to something more akin the Battle Tower/Boss Rush and grant the winner (aka player) a "wish" from limited choices as you suggested (implied to them using their tech which is obviously less powerful than Infinity Energy).
And good eye with the clothing shops!

That said, being there's a batch of them AND they're bunched up together, I think we're going to get clothing stores in the same vain as SV: Each store has a specialty, there's no interior just a menu, and if it's directly copy & paste than most clothes will be the same design just in different colors (GF, PLEASE, let us select the clothing design & then the color; you don't need to have every single design & color combo in a drop down menu).
Heavily digging the implication that having coffee and treats with your little fella is a game mechanic
*Eats a bacon sandwich as Tepig watches in horror*
... What? It's no one you know. Chikorita doesn't look at me like that when I eat a salad.
What I wonder is if we will be able to work somewhere, like we did in XY at the hotel.
(...)
EDIT: I can see our friend being Lyssandre's son or some stuff like that and winning the Z-A tour in order to get their wish granted - getting his father resurrected. Although this could very well be Arven too!
From what they said in the first trailer about exploring around Lumiose City it sounds like doing odd jobs and such would be part of the Daytime gameplay.
I never took Lysandre as someone having a family. Feels like during his young adult days he got fully focused with trying to help Kalos, grew jaded from the experience of selfish people, and became the man we say in XY.
Honestly the villain leaders who we know who have a kid feels like the only ones who would. Maxie, Archie & Colress are also too focused on their goals. Cyrus hates emotions. Ghetsis decided to adopt children for his evil plans. Guzma and Penny are too young. Piers too busy with his career and running Spikemuth (though maybe now Marnie is in charge he'll have time to date).
I'm just going to keep on seething that we'll never get fully realized PokeTokyo because they used it up on Game Boy map design they refuse to modernize
Well according to Bulbapedia the PokeTokyo would be both Celadon City and Saffron City (Celadon being the residential and Saffron the commercial center; also this would include Route 7 which Bulbapedia relates to a few parks but I don't see it). They're the two biggest cities in Kanto so if they were to do a redevelopment plan in Kanto...