The quest rewards are the same (except one minor Imperial glitch, but it's nothing you'll miss). The only difference is how certain people treat you - and usually that doesn't manifest until there is a clear winner in the war (end of the questline).
Dunmers would generally be against Ulfric (talk to the Dunmer in Windhelm and you'll see why), but my Dunmer warrior joined the Stormcloaks anyways and was warmly received and treated as an equal. Both sides dislike thievery (of course), but
Spoiler the Imperials have sideways ties to the Thieves Guild (through Maven Black Briar).
In the end, Imperial armor sells for more than Stormcloak armor, so I guess the more profitable would be Stormcloaks.