What religions do you think will be prominent in Skyrim? Temples to Ysmir, chapels to the Nine Divines, dragon worshiping cults, nature worshipers, Daedric cults, etc.
I think that chapels of the Nine Divines will be present but not in every town like in Cyrodiil. And if Skyrim proves to be a direct sequel in Oblivion then the fall of the Empire would affect how strong the influence and presence of the chapels is. Also being farther from the Imperial influence I expect a bigger attention to Daedric Gods like in Morrowind.