Honestly, it probably wasn't the best idea to give us a choice in the matter, because anything that comes in 5E, and involves Tamriel, will most likely be heavily reliant (from a historical perspective) of what happened in Skyrim. Something as major as, say, a force like the Empire being defeated, and losing an entire region (especially one as important as Skyrim) to a force comprised of what was essentially civilians, would be a huge conflict for history. Then you have the Aldmeri Dominion, whose reaction to Skyrim falling from Empire control would have to be integrated.
This is really what separates the game from the lore. If we weren't there, the war would have gone its natural path, and it would eventually end. I think it's safe to say the Empire would naturally have been victorious. If they weren't, it really wouldn't make sense, and throw off the history. The Stormcloaks was essentially makeshift army, comprised of mostly civilians that took up arms (some have military backgrounds). The Empire has been around for thousands of years, is a professional army, highly skilled in military tactics and strategy, economical sound with ties all over the continent, in a truce with the Aldmeri Dominion, and all around more capable. Not to mention that if the Stormcloaks won, they would void themselves from the treaty they were protected under with the Empire, and the Aldmeri Dominion would then conquer them. Ulfric would basically have led the country into a slaughter, and watched everyone die. This is why the Empire signed the treaty in the first place... it wasn't because they wanted to, it was because they were forced to, and had no other options if they wanted to spare the lives of the people. This is why Ulfric wasn't a fit leader. A leader has to be able to set aside their pride, and make hard decisions that are in the best interest for the people they serve. Maybe he, and those that joined his army, were willing to die fighting, but that doesn't mean everyone he would have served in SKyrim would have been. All Ulfric would have done is watch Skyrim fall into complete control of the very same force he despised, the Dominion, and the Nords of SKyrim would be dead. Good job, Ulfric.
Bethesda should have declared the war's victor. Although, like I said, there's the game, then there's the lore. If a title comes out in 5E, for example, they can still decide the victor for historical records. The Civil War would ultimately have just been a fun detail in the Skyrim title.