Honestly I don't see the balance reason behind the class only allowing 1 villian from Imperial and Merc.
How broken would Nemesis class be if you could pick 2 villians from same faction?
Why do you assume it's a balance reason that you can't pick them from the same faction?
Pick 2 mercenaries as villains, then play a mission which has Special Setup contain: No mercenary figures. 
Pick 2 mercenaries as villains, then play a mission which has Special Setup contain: No mercenary figures.
Yeah, that's what I was thinking- faction limitations is really the only balance issue I see, especially since you can only bring one villain per mission (so it's not like you can pick two that have really good synergy).
Why do you assume it's a balance reason that you can't pick them from the same faction?
This is probably a little more accurate. It's probably just to bring some flavor to the game. The class is called "nemesis" after all. Makes sense that there would be an Imperial Nemesis and a Merc Nemesis. If there were two of one faction, it wouldn't pack the same punch.
There is no limitation to villains in the same way as allies. You can use as many as you have earned and have open groups (and additional from Nemeses class cards) and threat for.
There is no limitation to villains in the same way as allies. You can use as many as you have earned and have open groups (and additional from Nemeses class cards) and threat for.
Ahh, I see. I was reading the Nemesis starting card as only allowing one of those cards to be added to your hand. It would actually mean that the first one added does not count toward open group That makes sense.