Might as well give 'em resistances or weakness to such moves. Blasters from the space animals could be considered Electric as well as a lot of Ganon's moves, there'l a lot of fire moves in Smash Bros. as is, etc. etc. That'd actually be pretty interesting and definitely make PT moar useful/mastering all of his Pokes almost mandatory in high level play.
... Hell, that's a brilliant idea. Switching Pokes to get resistances and lessen damage/knockback would make PT go up in tiers even if his Pokes weren't changed AT ALL.