Well, along the lines of "Why would Talos fight the empire?":
1. It's no longer of his bloodline. (No longer the Septim Empire, but rather the Mede Empire) He wouldn't likely have an issue with killing off an empire that has nothing to do with his bloodline anymore.
2. He's also possibly punishing the empire for removing his name from worship across Tamriel.
And isn't there a small connection between Talos and Alessia? Or am I just plain out insane?
And also, I don't see how it's so doubted. I mean, you have Ama Nin who was Mara in human form. I never really said that Ulfric is possibly Talos reborn, but rather a human manifestation of Talos to take back his homeland and punish the empire. Who knows? Perhaps it's MK's plan to bring Talos back and re-conquer the empire for the Septim bloodline again! lol
EDIT: I also see some of you saying that you think Tullius is more like Talos. My question is: why would he fight FOR the same empire that is not of his bloodline and of which stamped out his name in worship across Tamriel?
EDIT2: Also, you have Wulf who was a manifestation of Talos in Morrowind.