It is cool. I can see why a lot of people don't take sides at all, it's one of those conflicts where neither side is really right. Someone in Jarl Elisif's court mentions that High King Torygg (The guy Ulfric killed) really respected Ulfric and probably would have declared independence on his own had Ulfric not been so rash.
On one hand the Stormcloaks are right to be wary of foreign rule, especially when the Aldmeri Dominion is obviously running things behind the scenes, but at the same time Skyrim needs the Empire, and the ensuing civil war is just going to destabilize the Empire even more.
Two things I'm wondering about the next game:
1. Who will canonically win the war? This is the first time, as far as I know, that an Elder Scrolls game had two mutually exclusive quest lines with far-reaching impact on the series's storyline.
2. How bad is the situation going to be in TES6? The Empire's in deep shit, and I'm wondering how things will resolve themselves. I bet TES6 will be in Summurset Isles.
A late response, I know, but ah well.
1. They'll probably do something like Daggerfall where ALL the endings happened. i.e you got squished, a god was made, the orcs got a kingdom, and the various city-states were combined. Or the ending will be a combination...The Stormcloaks win the war, but are eventually defeated by Imperial reinforcements from Highrock and the Imerial Province.
2. People have been saying Summerset Isles (now Alinor) since Oblivion...Probably will be. Wished it was Blackmarsh and Elswyr in one game. That would be awesome with the the alien culture of the Saxheel and the khajits' religion and new slavehood under the Thalimor. Oh and yeah, deep shit. Especially if all this "Khajits being a Tower" being discussed on the lore forums are correct.