Maybe they're controlled by the villan team?
Or instead they need to be captured to finish the main story, like reshiram and zekrom
Remember Mewtwo? It hated humans because he thought that they were weak and selfish beings only interested in power and wealth; and it also despised the Pokémon who served humans. Whiiiich was kinda apparent on The First Pokemon Movie where he tried to capture every one of the trainer's pokemon. D=
Well, true, no pokemon are truly 'evil', but they would still have a 'lack of goodness'. I don't strike Xerneas and Yveltal as 'bad pokemon' too because they can still 'salvage' or represent and protect the isolated region of Gen 6 in their own way, but, still, the jury's still out on that one.
Fact: pokemon don't no how to use money ( meaning they can't be wealthy )