Okay, so I figured that the fighting would go something like this. It'll be like the show in that Pokemon can learn more than 4 moves, and it isn't necessarily turn-based, however, stronger attacks can only be learned by higher-level Pokemon, and each attack much stay accurate to the game. This means no "Thunder Armor" or blocking fire with Swords Dance, or anything like that. This also means no ridiculous combo attacks, like Solarbeam and Fire Blast. However, a single could do something like Double Team and an attack as a combo, or Quick Attack to get distance and then cancelling it, in order to go into a close-up attack.
That sound fair?
Well, in all honesty, I think that it would be ok in Double and Triple Battles if two Pokemon combined their attacks. I mean, that is sort of a new mechanic in the Gen V games anyways. Still, nothing stupid.
I also think we should be allowed to get somewhat creative with the Pokemon's capabilities. For example, like how in Pokemon Special, Blue's (the girl) Blastoise could fly by firing his water canons at the ground and stuff like that.
I would picture a kind of blend of the anime/manga style of battles, but at the same time following the rules of the game kind of closely. At least better than the anime does.
So yeah, no Thunder Armor or "Aim for the horn!" bullshit.
Basically, standard rules for any RPing that involves fighting: Don't godmod, and don't be an ass.
