I've played through TESV quite a few times, and even so, I still can't find a side in the civil war that I fully agree with. Here's my opinions on both sides:
The Empire is all well and good, but this isn't our beloved Septim Empire anymore. Granted, they aren't bad, but to me they just lack... well, a backbone. When the Thalmor were taking Elsweyr, the Empire was nowhere to be seen, they just left the Khajiit to their own devices. During the Great War, they actually /lost/ the Imperial City. Granted, there were exogent circumstances beyond their control, I know this, but how in the bloody hell do you actually allow your capitol to fall? They managed to take it back, and that was no mean feat, but directly after they just up and surrendered on the Thalmor's terms. With a display of that magnitude, they could have at least bargained to retain Talos worship, but they did not. I guess it bothers me that the sacrifice of the soldiers who died defending and reclaiming the Imperial City were just... worthless. Their deaths amounted to nothing, they would have been alive had these terms been accepted earlier, but now their all dead with nothing to show for their sacrifice. The Empires standpoints and actions are understandable I guess, but I cannot stand for a nation that just pisses on the sacrifice f those who risk everything to defend it. Furthermore, the Empire has always known about Argonian and Khajiit slavery in Morrowind, yet nothing had been done until the Argonians finally stood up and did something about it. There has been so much injustice to certain races that the Empire has always just allowed, and I'm finding it harder and harder to want to help them. I know slavery was eventually outlawed, but that really isn't something you get over quickly.
I have so many issues with these guys that it's not even funny. Let's start with Ulfric. He's a f---ing traitor first off, after being released by the Thalmor, he reclaimed Markarth when they told him to do so. He actually did a favor for the people who he fought against, it's written in black and white in his dossier. The only reason he hates them now is because, after declaring Talos worship legal, they locked him away for it. What does he do after that? He goes and kills the High King. He claims it was fair combat, but he issued the challenge, and before a response could be given, he used the Voice to nearly tear him to peices. Seeing he was still alive, he simply goes up and stabs him to death. And instead of defending his actions, he turns tail and runs away like a coward, proving it was nothing but cold-blooded murder. Moreover, he is just a f---ing racist. He forces the Argonians to live in a freaking warehouse on the docks and keeps the Dark Elves sequestered in an impoverished slum. He knows of the injustice in his city, but he turns a blind eye to it, why? Is it because he's busy? Or maybe t's because it's Nords oppressing non-Nords? Who knows? He is so fine with racism that he actually tolerates his men showing it, hence Stormcloaks throwing around the term "lizard" when I run into them. Ulfric is a liar, a coward, and a murderer. He isn't fit to be High King, and his claims are completely illegitimate.
I guess there really isn't a good guy. Nobody is perfect, it's really just a matter of deciding which is the lesser evil to you. I wound up choosing the Stormcloaks, not because I like them, I hate both sides equally. I chose them because it came down to "which armor looks better?", and the won. I'm curious as to what side you chose, and if you have a counter-argument for anything I've stated, I'd like to hear it. If you want to prove something I said as false, I'm all ears, but until somebody does, I just hate everyone.