I've done both. I play a Dunmer and both have kinda good reasons for siding with both. 

Stormcloaks:
The Empire has been terrible for the people of Morrowind and abandoned us when we needed them.
After the Khajiit tore through Morrowind the Stormcloak racism towards, at the least the Khajiit is something my Dunmer can appreciate and be happy about. Also my people know the feeling of having our own homeland taken from us. 
You could also say your Dunmer is sympathetic to the Thalmor cause. I never was. Fuck the Thalmor.

Empire:
If you are pivotal in the Empire's victory there is a chance you can use your influence to get Imperial aid for your people back on Morrowind. 
The Stormcloaks treat your fellow Dunmer like shit, and fuck that.
My Dunmer was one who loved great power, and securing the Empire foothold in Skyrim ensures that the Empire is still very strong, this is especially good if the Thalmor attack again, and again fuck the Thalmor. I've never been a fan of the Thalmor as a Dark Elf. I think they take the idea of being a mer and bastardize it with the Thalmor. Also Dunmer> all other mer.