Let's say after you get the amulet, and you are going through the sewers, a member of the Mythic Dawn comes towards you and starts talking. There are two options.
1) Help him, and help the Mythic Dawn.
2)Kill him, and follow the original MQ.
Not only would this add variation to your gameplay, but would also add more time in wanting to play Skyrim (even though I intended to play it a lot anyway).
Now obviously, this would have an affect on the world in which the game is implemented into. If you go with the good side, good things would happen to the kingdom, and the opposite effect for the evil side.
This is pretty much for the classic Good v Evil feel of classic RPG's.