We know the CoW and the Synod replaced the Mages Guild, but I wouldn't yet consider them a certainty for Skyrim. The CoW and Synod are Imperial institutions, and we can't really know what sort of Imperial presence will exist in Skyrim.
If they do turn up in the game, it will be interesting to see how they differ from one another. Infernal City was vague on the details, so the only thing we have that approaches a 'hint' is that, from what I understand, the word "synod" has a religious connotation.