I definitely don't think we'll see either the Legion (if we do, it will be in very small numbers) or the Imperial Trading Company. As far as I know, the Empire is pretty much rather far out of the picture.
The Empire presence will probaly be limited to an embassy in the Skyrim capitol
some guild ideas
-Mercenaries Guild (or club or something), Their headquarters should be a pub or something, and you don't et quests from the guild members, you are approached directly by customers, or they could do it like th eTheives guild in Oblivion, where you freelance for a while, and get special jobs
-Instead of the Thieves guild being like it was in Oblivion, it should function like the Mockers in the Riftwar books,
-Daedric cults, you offer your service to a Daedric prince of your choice, and get quests from the head honcho, eventually becoming the Daedric Princes, 'mouth' in Skyrim