I voted for the option of a chance to join the evil team.
Not sure if X and Y will be different, but most of the Pokemon games tend to be a bit too linear. As in, there's only really one place you can go to continue the story, and if you try to go somewhere else the game says "Sorry, this bridge is closed for maintenance." or "You have to get this gym badge to pass through." or "You can only access certain parts of the area by passing over terrain/water if you have a certain HM."
So being able to have the option to change the story in some way that you see fit, whether it's becoming evil, or wanting to challenge the 6th gym leader before you've defeated the 3rd gym leader, I think would be a big step.
Besides, just because you're evil doesn't mean you can't still fight the gym leaders and become the League Champion. Someone let Giovanni be a gym leader, and he's evil. So why aren't we allowed to be evil, steal Pokemon and cause havoc for upcoming NPC trainers?