I read the history of the Vampire Counts again and I still see no reason why Nagash should be a Leeader of them. As I read it Nagash was a renegade Priest in the city states of Nehekhara and responbible for their undead existence. His necromancy also lead to the creation of the first Vampires but the Carstein don't seem to be related directly to him in any way. More likly they descent from a bloodline of renegade Vampires and Nagash seems to be mostly related to Nhekhara and Lahmia for the whole time of his (un-)life. I think he better won't make part of any civ. His status seems to be kind of a Demi-God, the first Necromancer and Creeator of undead beings but he never ruled a whole civilization as far as I can read out of this lines. He tried too but was defeated.
If we are going to have him in the game I suggest only as a Hero Unit or Leader in a scenario.
Second Leader for the Vampire Counts could as well be Manfred von Carstein.