As for me, I'd like to be able to join any and all villainous organizations. Many people have characters that are Outcast, Lost or even Nemesis members(At least in their own histories). I personally feel it would make for a great deal of new content and some nice quality of life if I could hitch my wagon to most any villain group. We have official Arachnos arch-types with the I12 villain epics, this would and could be for the lower levels.
Create a villain and seek out a member of Nemesis (A contact) and get from him a mission to prove your worth. From there you take on additional missions themed to the villain group in question earning temp powers, costume pieces and so forth. Until eventually you are made a full member serving in the upper echelons of the group. Stretch it out reasonably and it would keep more then a few people entertained for a good long time.
Now I've put no thought into coding and so forth. I have no idea how hard any of this would be but I still felt that it was worth posting. I cannot see this if done properly, would ever be a bad idea. Of course I think heroes should get this too....join Longbow, earn a uniform and costume slot to put it on.....a jetpack, able to call in back up.....ah I'm just rambling now.