The only way I could even possibly see them allowing us to join the evil team is if Pokemon became an MMORPG or something of that sort...
Although I do agree that it'd be incredibly fun to hang out with Jessie, James and Meowth (or whatever our evil team buddies would be) I just can't see it happening :/ I think it'd be cool if you started off a game as a part of an evil organization, but it put you in a good light and you didn't realize you were a part of Team Rocket or Team Plasma until the very end or something... but I doubt that be rated E for everyone, and is probably too risky of a business move.
Joining a team undercover would be awesome as well! We'd be like the (I guess kind of BW2 spoilers but not really?)