This suggestion isn't for the main game, but it is for the online Battle simulator (and probably also for the online battles in the normal game).
Allow for pokemon that have alternate forms that are significantly different from each other (ex Rotom, Wormadam) to appear multiple times in a party, but not pokemon with alternate forms that are essentially the exact same (ex Unown, Vivillion, Flabébé [if those last two ever get added]), just have different stat distributions (ex Deoxys) or have better stats like a mega (ex Giratina, Kyurem).
(Honestly, I'm just kinda annoyed, because I just spent 2 hours making a pretty good Rotom team and I can't use it)