You know, to avoid folks going on a rampage with a Mewtwo-driven sleigh, they could implement some kinda points-based system, ala tabletop wargames like Warhammer. Personally, I'd get sick of every PvP match involving legendary birds and/or dogs. Zapdos=tons o' points, Parasect=not so many.
But then again, that would definitely complicate things, and sort of change the fundamental basis of Pokemon. Deep in my heart, I've wanted to see a comlplex Pokemon game that played out something like Gladius, but that would shoo away a lot of the core demographic, I suppose.