you could fight for one side anyway since once you chose that was it.
Civil war would be good for vampires, three factions and three sub-factions within each.
The main factions should be like a civil war about what vampires should do, one side may believe they should rule skyrim openly and brutally, one side may want to simply co-exist with mankind again openly and the third may wish to keep their existence hidden and never live openly.
Now the sub-factions should be simply class types, warrior, mage, stealth and each one gives a bonus unique for each sub-faction.
I meant that it would be bad to only allow the player to play on side instead of choosing between the two. As in force the player to fight for the Stormcloack with no possibility of even joining the Empire.
Two or three would be just fine. A more barbaric clan that would attempt to take over by brute force, as you said. And a hidden one who is more politically inclined and civilized. I don't agree with the coexisting with humans thing. We have that stuff for werewolves already.
It's like saying a bat would coexist with their favorite food.