While I think this would belong in Gameplay Ideas, I will still post here regardless.
I would like to see a more pernicious team than these toothless mockeries that we've been receiving. Team Rocket was nothing more than hot air, and while Teams Aqua and Magma did pose some vague threat to the world, they were hardly to the level of viciousness that I would expect from a truly evil team. Now now, I'm not asking for a team that goes around committing wanton acts of murder, but I have yet to see a team perform some serious crime. And no, stealing Pogeymanz doesn't count. >_>
Rather, this team should actually be ambitious about its goals. If they need to burn down the police station to stop their goals, so let them. Should they have to detain the protagonist, so let them. In fact, that would make a pretty neat plot twist if you were suddenly kidnapped by this team and you had to escape from a labyrinth in which they dumped you.
With all of that being said, my primary desire is to shatter this glass wall of morality through which these "evil" teams refuse to break.