My only issue that I think about with a "Dark Avatar" is just the fact that Vaatu would be reincarnated. Period. He would not have all four elements to bend. Raava was the one who collected the other elements from the Lion Turtles and she is the one holding onto all four at once. As far as we know, Vaatu has not collected any from the Lion Turtles. That's my only drawback about the whole thing.
Spoiler
I know it doesn't make sense but I bet they'll do something so he can get them, that or what I told my brother, what if he ends up in the body of a earth/fire/air bender once he reincarnates, more than likely he would still have water plus the new element so all he would need to to reincarnate 3 times and he would have all the powers.