If there's one thing we know about the Prime Evils, it's that they are constantly scheming against each other for supreme dominance. I wouldn't be shocked to learn that such a conflict is currently raging within Prime Evil Diablo, so how about a fight where during each phase one of them assumes "control" of Prime Evil Diablo's body/appearance, allowing us to fight all the Prime Evils in one epic battle?
Edit: I also want to add that from a storytelling perspective it is totally normal to go back to the "original" villain in the third act, so it kinda does make sense for Diablo himself to return for the "final" kill in the last part of Diablo III. Also, will there even BE a Diablo IV? If so, probably not for 10+ years at least. If not, then it's extra important that the last boss ever in the series should be Diablo again.
Things could have changed, but the company line from early on was that Diablo 3 will wrap up the storyline started by Diablo 1 (the prime evils trying to corrupt the nephalem/Diablo's scheme to become the one Prime/Diablo becoming Tathamet again/whatever), but it would not be the end of the Diablo universe.