I go stormcloak. Always.
1)They are probably the least racist. Windhelm has the largest dark elf population in the game, and the only mistreatment they get is from a pair of drunks. This level of tolerance is incredible considering the majority of dark elves are slavers, as bigoted as the Thalmor high elves, and enthusiastic deadra worshipers. The argonians aren't let in because many of them are thieves and the dark elves have a long history of enslaving them, who needs that kind of racial tension?
2)The Aldmeri aren't going to take over the world. After the war they were given land in Hammerfell, the redguards left the empire and defeated the army sent to secure those lands. Seems like the Aldmeri Dominion is not the incredible juggernaut of conquest the fearmongering imperials make them out to be.
3)This is a continuation of 2: If Hammerfell was able to win against the elves alone, why did the empire give up so easily? If they had stuck it out they could have broken the Dominion. Instead they folded a winning hand. I don't prefer siding with losers.
4)The empire tries to kill the player at the beginning of the game. Your BFF in the empire(hadrid?) even openly admits that you shouldn't be executed, but doesn't actually do or say anything on your behalf. Alduin, the villain of the game, does more to save your hide than that prick.
5)The empire's laws are a joke. When you later meet Tullius, the general you presided over your near execution, he just says: "Well I know we were going to execute you, but it seems like we didn't have a good reason to and I surely won't be consistent on this." The empire also allowed a foreign power to write and enforce a law inside it's borders, which is essentially giving up sovereignty.
TLDR: Stormcloaks are tolerant, Aldmeri are overrated, empire is a loser, empire is a jerk, and empire is corrupt.