Decisions in game have no consequences. You can be both the thieves guild master and the thane of riften and you can't kill any core npc's because you need them for (x) quest. It would be nice for (x) quest to be out of the option if you accidentally kill that npc. Or for dialog options to have the same affect, if you are caught stealing too many times or lying, certain factions will/won't let you into their guild. Main quest still a default but who joins you and what perks you have depending on what path you took in the side quests