Huh, happened across a fangame I'd never heard of, gave it a shot... and it's pretty damned good. Called Super Pokemon Eevee Edtion. The premise is basically GenII (with a seriously shaken-up map) blended with a lot of mechanical changes and a total overhaul of combat that basically replaces the Pokemon system with Final Fantasy. Here's a breakdown of most of what I've seen so far.
The starter is an Eevee which (with a key item) can transform between any of its eeveelutions both in and out of battle - you start with the base form, Volteon, and Vaporeon, gaining the others at some point in the future. This is less OP and more important than it sounds initially, because...
You can't catch wild pokemon. "Pokeball shortage", they say. There are two ways to get more 'mons: story progression (you get to choose one of the GenII starters after beating a pretty decent challenge in the first city you get to, incidentally not the gym), and (after concluding that sequence) by battling "corrupted" 'mons which appear rarely(?) in the world (rather than random encounters in grass) and using a key item on them to revert them to their normal forms after defeating them. Other than that, I only know that you can come back to that place in the late-game (it recommends post-Gym 5) and fight a tough battle for a second of the GenII starters.
Battles, as mentioned above, are FF-style; your maximum party size is limited to four 'mons. Here's what they look like, taken from the first gym leader:
A lot of moves have been adjusted for this, stuff like Sand Attack and Smokescreen affect the whole enemy party, for example. The type chart and (as far as I can tell) learnsets remain unaltered from GenII. Graphics are better though. There is no move limit. They accumulate like FF spells: you can have as many as possible on a 'mon, and use any of them in battle. Time bars are present, and fill according to each 'mon's speed. Limit starts when a 'mon drops below 25% HP. Most crowd control moves (though now AoE) have a markedly lower chance of hitting, apparently - Cynda's Smokescreen was only 30%.
From what I can tell, there are no HMs, all that is put into items instead. You get the bike from the start of the game, same with PC storage access for 'mons.
Battles have a chance of dropping "trash" loot items which you can refine at Pokecenters into item progressions which conclude with producing TMs, vitamins, &c.
Berries are less shit - they almost all give HP, PP,
and cure a status condition, or something similar. No planting of them though, as far as I can tell.
Oh, and PP is treated like MP in other RPGs. Your 'mons each have PP pools, every move requires a specific amount to use, and every 'mon has a four-turn-lock "recharge" move that refills their PP.
I was dubious about the concept, but... it's actually very, very cool. Still very much a Pokemon game, but with all of the OCD 'mon training bullshit and easy 'mon acquirement removed, combined with a combat system which is much more satisfying (IMO) and more plot stuff going on. Dialogue is a little too meta-jokey at times, but eh. The full-party battles definitely shake things up, there's a lot more value in having a varied team with support moves, and none of the usual swap-spamming cheese strats.
Also no fucking sylph scope and wiki needed to find hidden items, they have a small (but visible) sprite of disturbed ground that you can see with your bare eyes if you're paying attention.