Out of all the various mechanics and additions I've seen from fan games, the ones that always jump out to me are those that are crazy and unique yet are still reasonably possible in an official game. The idea of regional variants is one of them, and it was one of those ideas that everyone was generally in approval of.
Another similar category of those mechanics are those that actively try to improve mechanics that are present in the game already. These are usually the new types, new Mega and forms, new moves and abilities, and changes to how a Pokemon is trained with Effort Values and Individual Values.
But the idea of mechanics in general, at least in my perspective, generally make all of Pokemon fan games fall into two categories: games that play safe with a few changes, or games that try to go drastic, just chucking in a bunch of mechanics and Mega and moves and mini games and etc. (blame
@Atomic Reactor for the analogy!)
The games that I try to find are either the extreme end of the drastic, where it's arguable that they're a different game in their entirety and could be independent games by themselves, or the games that are the sweet spot between the drastic and the safe, where they find the right balance of the two.
As for me and my ideas personally, I'm right now trying to explore the idea where a player could easily flip between using the party for turn-based battles and using the player avatar/character to battle akin to Kingdom Hearts: Chain of Memories (minus the cards). As of now I have so many ways of approaching that that I would
love for anyone to add input into that idea in general, especially in the field of how to make that more fluid and not enter Sonic: Unleashed territory where you enjoy the speedy parts but want to just get the beat-em-up parts over with already.
And
@GamingGravey, I don't think that just adding the mechanic in general ruins a game, it's
how you add the mechanic. Take for example the idea of combining the best of the Join Avenue with the best of the PSS. What we got was the Festival Plaza, and we all know how people generally feel about that.