Hopefully, it's not too late to get this idea thrown into the mix. When I think of going rogue, one scenario that really clicks with me is the idea of a hero having to infiltrate a criminal organization. Trying to accomplish heroic objectives while needing to participate in criminal activities, or likewise working to bring down a group of heroes while appearing to serve the public, could create some very interesting shades of gray in the game. It definitely would appeal to the role-players.
Of course, part of the trick would be creating arcs that fit logically with different archetypes, so that the scenarios would truly challenge the player's notions of their role; for instance, a warshade having to infiltrate the Council. The other trick would be opening up costume options to have a costume that fit with the group being infiltrated. Last but not least, there would have to be consequences for being found out--could be as simple as closing the arc early, as complex as merit "penalties", or some other dimension of consequence.
Finally, this option could be useful in opening up the PVP zones for extended story arcs.
Cheers.
