Hard to say how this would play out. But starting with the combatants:
The Aldmeri Dominion: Summerset Isles, Valenwood, Elsweyr. Lot of military power here; the Altmer being arguably the best mages there are, the Bosmer being excellent archers, and the Khajiit filling the role of rank and file soldiers, spies, and assassins. Commanded by Altmer, intelligent and with CENTURIES of experience. They nearly destroyed the Empire once before, they certainly may succeed this time.
The Empire: Cyrodill, Daggerfall (I'm leaving out Skyrim, reasons to follow) Again, there is real power here. The Imperial Legion has a legacy of being Tamriel's greatest military force, and its for a reason. Excellent organization, tactics and discipline. Obviously not what it one was but still a force to be reckoned with. The Imperials built and ran not only the Legion, but the whole Empire, which did rule the whole continent for a long time. The Bretons are some of Tamriel's best mages, only rivaled by the Altmer. Even though they got thoroughly thrashed by the Dominion the first time, they still managed to survive and even push back the Dominion.
Now for the wild cards.
Black Marsh: Probably wouldn't even get involved, and I doubt either the Empire or the Dominion would try and take them on. They don't seem to care for the politics of Tamriel, more interested in their own affairs with the Dunmer. I say neutral.
Morrowind: Neutral, because their country blew up :P
In all seriousness, the Dunmer are in no position to aid either side after what happened with the Red Mountain.
Skyrim: Biggest wild card without a doubt. The outcome of the Stormcloak Rebellion has such a huge impact on a Great War II. Imperial victory: Nordic warriors supporting the Empire, along with access to Skyrim's vast resources. Big boost to the Empire. Stormcloak victory: an Imperial ally at best, and even then, I think only for the duration of the war. Depends on what ending is considered canon.
Hammerfell: Imperial ally. I think if real war broke out, the Redguards would be willing to help against the elves if it meant they wouldn't be next on the Dominion hit list.
But at the end of the day, I have to give my edge to the Dominion. Strong internally and externally. The Empire just seems to be a mess, There are even members of the Elder Council plotting to kill the Emperor, and the Legion's inability to crush the comparatively ill equipped and financed Stormcloaks makes me doubt the could take on a force like the Dominion.