So in Pokemon Colosseum and XD Gale of Darkness the evil teams are trying to make pokemon stronger by turning them into shadow pokemon. Through out the game this is shown as being bad because it closes the pokemons heart or some bullshit like that. So in X/Y you can mega evolve pokemon to make them stronger and it's considered a good thing for some reason.

Could it be that the villains in Colosseum and XD were actually just trying to mega evolve pokemon and release their true potential and the protagonist was just halting progress?