Tbh, I’d like to see a Pokemon game where the supposed “evil team” are revealed to be genuine good guys (or at the very least, just extreme in their actions, but are well-meaning with a pretty well-thought out plan on what to do afterwards) and from then on, the plot shifts from you stopping the “evil team” to working with the “evil team” to stop the true bad guys of the game (probably a corrupt Pokemon league, a mega-corp, or something other than those two).