PPS: There will be spoilers in this. You have been warned.
PS: This could get a bit rambly, I write as things pop into my mind, and my though process isn't what you would call "organized", nor am I particularly good at proof-reading what I write. I'll try to structure things properly and such, but I make no promises. With that out of the way, please enjoy my verbal masonry.
OK, so the last months there have been a lot of blogs regarding the Civil War. There was even a poll on the front page on which faction you preferred. If I remember correctly, the votes were split more-or-less 50/50. And I don't see why. I really don't. I'm probably just being myopic here, but I don't see how anyone, after having played the game extensively, would consider the Stormcloaks to be in the right.
Don't get me wrong, from the get-go I understand why the Stormcloaks would seem like the good guys, especially for players new to The Elder Scrolls. You are about to be executed for crimes you didn't commit (Well, you did commit a crime, but illegally passing the border hardly warrants the death penalty). While they make Hadvar out to be sort of a "good guy", it makes sense for the player to favour the Stormcloaks, as they leave a better first impression. From there on out, though, things start going down-hill.
The great war ended with the empire outlawing Talos worship (amongst other things), which is the basis of the conflict. The Stormcloaks didn't like this much. However, the alternative was fighting war they had assessed they weren't going to win. The stormcloaks, in other words, basically mean that having the entire Empire collapse would be better than giving up the worship of Talos. Not only is he worshipped for creating the empire (meaning that worshipping him would be kinda pointless, since there wouldn't be any empire), but he also only makes up 1/9th of their pantheon. Admittedly a lot of Nords considered him the most important God, but still. It's also worth mentioning that Talos is an aedric god, meaning he barely does anything. For most, not being able to worship him wouldn't change much. Finally, they (The Empire & The Thalmor) didn't start to crack down on Talos worship until after Ulfric made a fuss about it; up until that point everyone still had their own little shrines.
Then we get to their racism and bigotry. They treat other races, especially the mer and beasts, like dung. Windhelm is a great example of that; the dunmer live in a ghetto, and the argonians aren't even allowed to live within the city-walls. The jarl, good 'ol Stormcloak himself, meanwhile turns a blind eye to this, and even to crimes committed against them. Our heroes, guys and gals. Great people!
That said; yes, you can join the Stormcloaks even if you're not a nord. That doesn't make much sense, and personally I think it was done just so that most races weren't cut off from an entire quest-line. After all, Skyrim's take on races seem to be that they shouldn't matter gameplay-wise. That's just conjecture on my part, though.
There's also the matter of the Ulfric being somewhat under the Thalmor's influence, judging by the Thalmor report you can find on him during "Diplomatic Immunity". Don't quote me on this one, however: I only vaguely remember what was in that report.
And what of the long-term consequences? Without Skyrim, the Empire would be severely weakened, leaving them open for a new Thalmor invasion. And with Skyrim being on their own, they would be easy pickings.
That's not to say the Empire is flawless. For one thing, the Legion seems to have gotten more than a little execution-happy. But considering the stakes, it is, if not excusable, at least somewhat understandable. Overall, they seem like a stronger, more stable long-term choice.
Well, there you go. Those were my two ears. I just don't see how you can justify risking an entire empire for the sake of (part of) your religion. And they're racist biggots. That doesn't exactly make me think more highly of them. But what do you guys think? A crown for your thoughts. Also, sorry if there've been blogs like this one before. But seeing as I haven't found a satisfactory answer to this, I thought I'd write a blog of my own.
PS: The last part contained two horrible money-related translation jokes. Just ignore that...
PPS: The "PPS" and "PS" at the start stand for "Pre-Pre-Script" and "Pre-Script" respectively, while the "PS" and "PPS" here at the end stands for "Post-Script" and "Post-Post-Script". Didn't know what to call the thingies at the top, so that's what I went with. Kinda unorthodox, so I felt I had to explain myself. So, um... Yeah. That's all, folks!
tl;dr: "Stormcloaks vs Empire" is "Black vs White", not "Gray vs Grey" (morally ambiguous). In my opinion.