In an article I read, I remember reading that all the Nine Divines and same Daedric gods were still in Skyrim. In this case, Hircine would be in control of the werewolves if they were in the game right? And if the Thieves guild is still here, is the Gray Fox and Nocturnal's cowl still here to? How would they work out Sheogorath, did the old one take over the players body over time and eventually gain his old appearance or what? Could you guys try to giveme answers on these three questions, I seem to be confused.
1) Yes. Hircine would still be in control of the werewolves and perhaps werebears if they are in the game.
2) The thieves guild has different branches which seem to be completely separate from cyrodiil's. Nocturnal's cowl might come back by some circumstance though.
3) I doubt they would change CoC's position as Sheogorath (It makes the actions of Shivering Isles look worthless). If there is a statue in Skyrim, I bet the voice will be Haskil.