How will Beth decide which is canon, the Imperial or Stormcloak victory? It's obvious there is going to be another TES and it's too major for them to give no explanation. Warp in the North caused by dragons [censored] with time?

There are some previous threads that discuss the possibilities. One such thread:

http://www.gamesas.com/topic/1475039-pro-empire-or-pro-rebels/

[Edited link to remove highlights in thread text. Sorry ]

One solution: Have something happen that makes it a moot point who won the war.

Mhm. It'd feel so forced and silly though. How come no one seems to remember and care about who won the war? How come we don't find any books talking about the civil war and its aftermath, instead of just skipping to the thing that happened after?

Depends entirely on the execution. They could also choose either side.

For example, the Storm Cloaks win out eventually and Skyrim becomes a free-state. But a book mentions that both Tulius and Ulfric die in the war. So it could be that you side with Ulfric, win, and then he gets killed but Skyrim stays free. Or it could be that you sided with Tulius, but then he dies and the Stormcloaks (sans Ulfric) win anyway, over time.

Alternatively, there is a Second Great war. Either the Thalmor cripple the Empire and the Imperial troops are force to leave Skyrim (regardless of who won the civil war.) Or, all of the human provinces rally together to fight the Dominion and Skyrim becomes part of the Empire (regardless of who won the war.)

Without using the internet, how many coalitions did Napoleon defeat before he was soundly trounced?

See how easy that works?

I'm tentative about the Civil War actually ever happening (what we get in game is to me rather wooden-feeling, I'd rather take it as an anology for some real conflict in Skyrim during that time, which we only know little of). But assuming that there are such characters as Tulius and Ulfric,

This is a really good way of putting it, and moreover explains why I don't even need to know whether the Civil War is real or not.