Apologies for the lack of updates: I had been doing another run of the game to try and get a better picture of some of the borderline mons on the tiering list. The team I used to clear the game was Vaporeon/Houndour/Shroomish/Elekid/Natu/Zangoose, with Salamence Master Balled for the Greevil fight. In terms of optional battles I cleared the first two areas of Mt. Battle (Water Pulse TM + purify Natu), one run of Pyrite Colosseum (purify Shroomish + Brick Break TM), and two runs of Realgam Colosseum (lategame EXP + Giga Drain TM). My run of the game was not particularly difficult save for Ardos, to whom I would have wiped had it not been for a timely Focus Band proc on Houndoom and some confusion hax against his Snorlax (lol). I don't have much to say about Houndour or Salamence - I think S-tier and E-tier are fine for them both and these aren't really contested, so let's focus on the other four.
Vaporeon - I went into this run believing Vaporeon was a borderline A/B mon, and I still think that having finished the game. However, I think Vaporeon is now closer to A-tier than B-tier. Vaporeon tanks hits like a champion and fights back with a good mix of offensive and supporting capabilities. While Water Pulse as the best STAB option is meh, even Water Pulse hurts when its coming off 110 SpA (which is way better than what the other Water-types in this game have to work with), and backed with Ice Beam and Bite I found Vaporeon was still able to at least 2HKO a lot of its opponents well into Citadark Isle. I didn't go for relearner Helping Hand due to not feeling like grinding for the coupons, so instead I gave it the Icy Wind tutor from Agate Village and it served me very well, being an incredibly good early coverage move as well as a strong late-game speed control option that partially made up for Vaporeon's low Speed (and also saved me against an otherwise horrendous Ardos fight). Vaporeon has a pretty commanding performance through Snagem Hideout and only starts to lose a bit of steam near the end of Cipher Key Lair, but it still does well enough and Eldes/Greevil don't exactly appreciate a fat Water-type hurling 110 SpA Ice Beams at their very Ice weak teams. I was pleased with Vaporeon's performance and would thus be willing to raise it to A-rank, the Speed and weakish STAB options were still kind of annoying but Icy Wind and its raw SpA helps compensate for its flaws.
Shroomish - I think Shroomish is a solid Pokemon worthy of A-rank, but I do not think it is worthy of S-rank. Breloom dominates midgame extremely hard, but a combination of a poor early period and a lot of rough matchups in Citadark Isle keep it from being S. Shroomish is really bad when you first get it - it unfortunately comes at the tail end of a Water-heavy Shadow Lab when the level curve is starting to increasing, and though it takes hits okay it is sorely lacking in power and thus needs some grinding to catch up. Once it becomes Breloom and gets the Brick Break TM it becomes a monster and will basically wreck everything through ONBS and Phenac City with a mostly strong performance in Snagem Hideout and Cipher Key Lair. Citadark Isle is where things start turning against Breloom. There is a rather annoyingly high number of Pokemon that can prey on its weaknesses, its mediocre Speed starts becoming a problem, and its matchup against the toughest endgame bosses is pretty bad, with Ardos, Eldes, and Greevil packing multiple ways to body Breloom before it can do much. It's still a good Pokemon and it's not like its endgame contributions were bad, but it was probably the Pokemon on my team that also died the most and that's not really what you would expect out of an S-rank Pokemon. I think keeping it at A-rank is fine. It's performance is overall great but its early period is kinda awful and lategame can be rather tough on it.
Natu - Natu is currently B-rank and I stand by that ranking after using it. Psychic-types are very good in this game and Natu is no exception, boasting a nice STAB Psychic off acceptable offenses. It's also defensively surprisingly decent, with access to TMable Screens it makes solid use of from its good Speed, and it's Ground-immunity makes it a very nice mon to pair with Earthquake users (shame I didn't get any in this run, oops). Its offense is kind of weak until you get the Psychic TM, but there are a nice number of Grass-types to use Aerial Ace on until then and Screens are always useful. I consider it to be about on par with Lunatone - Lunatone has less of a dead period and better coverage with Ice Beam access, but Xatu has the same strength behind its Psychic, much better Speed, and a small availability lead. Screens and a decent Psychic allowed it to contribute to basically every boss fight.
I actually think Natu's performance is a good argument to raise Ralts to A. Ralts arguably has a longer dead period than Natu but also has an availability lead and Gardevoir is far, far more offensively potent while keeping Screens and even a sleep move (though its inaccurate). I think as far as the Psychic mons go in this game its Espeon > Ralts > Natu=Lunatone so I think raising Ralts to A would better reflect how they all stand.
Elekid - Going to go ahead and say Elekid should rise to A-rank. The main arguments against it are that it comes late and underleveled and also purifying Togepi is a bit of a hassle. The latter is not too hard to do by spamming scents (which you should have plenty of money for by that point) and the former is easily worked around by giving it the EXP Share through Snagem Hideout. You can argue this is favortism, but Elekid benefits from Trade boosted EXP so you don't have to give it that much attention and it should reach Electabuzz by the end of Snagem Hideout. At that point Zaprong becomes outstanding, with unparalleled coverage that allow it to destroy the rest of the game as it continues to snowball with that sweet sweet trade boosted EXP. Like Vaporeon its a borderline A/B mon to me, but its performance was strong enough to where I'd say it should be A rank.
Zangoose - I was kind of disappointed by Zangoose. Admittedly I had a bad nature (Relaxed) and didn't get Swords Dance (too expensive, I gave it Double Edge instead), and it's not bad, but it's not outstanding either. It has pretty good damage output and coverage between Body Slam, Brick Break and Shadow Ball, but it doesn't have Ursaring's overwhelming strength either unboosted and it doesn't really contribute anything defensively due to no useful resists and pretty bad defenses. It doesn't have a particularly great performance in any major fight in Citadark either, usually only being able to trade itself to kill or heavily damage something before going down. It's not a bad Pokemon but it's definitely not A-rank material I think.
tl;dr Vaporeon, Elekid, and Ralts could probably go up to A
I'll do some updates in a few days.