When I first heard this idea, I thought it would have been a good story as well, but then thinking about the logistics, I don't think it would work.
Imagine you have people watching Negan over multiple seasons, viewers get to know and start to identify with the characters. They see the history, the backgrounds, and the events that build up to him becoming what he is. Similar to what Rick now is. He is no longer clearly the "good guy" He just does what he needs to survive. The same is likely true for Negan. Now they meet Rick's group. Who is going to win?
You probably have an epic build up and an epic couple of episodes, but then what? You have a similar problem to the face vs face problem you talked about in the Wrestling thread. There is no longer a clear cut bad guy for the audience to "cheer" against. Pockets of fans are going to be "cheering" for different characters in both the groups. Then after the fight and one faction "wins", can you still really continue with two different series?
As to FTWD itself, I stopped watching after 2 - 3 episodes. It just wan't compelling enough to keep watching for me.