I heard rumors of not only the imperial/stormcloak but also thieves guild dark brotherhood. If you completed the brotherhood before you join the thieves guild then you can't join the guild. Unsure of if it's true or not.
When I play Skyrim I want to do ALL quests and join every guild in the game and collect all what should be collected(or not^^). That you couldn't do in FNV but I remember that we could do that in Oblivion (don't know anymore if thats true)
You couldn't do it in Morrowind, either. Some feel that closed doors promote replay. Anyway, I hope the major content isn't so limited that a few closed doors make playthroughs feel trivial.