Really, how many games let you play the 'bad guy'? The playable character typically has some sort of motivation. If someone just wants to catch other people's pokemon, Colosseum and XD should be enough. Otherwise, the evil plots consist of "Get lots of money" and "Get Legendary Pokemon"; things which the games readily allow.
Though, to be fair, the evil plots are decidedly straying into "Destroy the World" territory. However, when you're the strongest trainer, and can farm the Elite Four, is there any difference between you and, say, Team Plasma? After beating most trainers, they won't fight you again. In a plot about fantasy gun control, you've got nukes. You can become the champion, which is pretty much the equivalent of ruling the world. Do you really NEED to play an evil character?
Though, to be fair, the evil plots are decidedly straying into "Destroy the World" territory. However, when you're the strongest trainer, and can farm the Elite Four, is there any difference between you and, say, Team Plasma? After beating most trainers, they won't fight you again. In a plot about fantasy gun control, you've got nukes. You can become the champion, which is pretty much the equivalent of ruling the world. Do you really NEED to play an evil character?