Pro-Imperial:
1) I'm Altmeri and from what I understand the Stormcloaks are racist against all other races.
2) I'm married to an Imperial, Marcurio.
3) Both me and my husband are Mages, and the Nord are not fond of our kind.
4) I'm Arch-Mage of Winterhold College, and have to look out for the interests of my school.
5) The Rebellion is weaking the Empire which could lead to the Second Aldmeri Dominion invading and Skyrim falling to them anyways.
Pro-Stormcloaks
1) The Nord should have the right to self-governance.
2) The alliance with the Thalmor could lead to further persecution of the people of Skyrim.
3) It's probably the "right" thing to do.
I guess I have more self-interested reasons for supporting the Empire, but is it the right thing to do?