Purely subjective:
-The best main quest story
I felt the Thieve's Guild ha the better story, but dark brotherhood had the better characters.
Thieve's Guild. Can quest to improve it, some useful stuff. No guild master's quarters though, AFAIK, so if you're in to that kind of stuff, darkbro' has you covered.
dark brotherhood, only and completely - If you use daggers that is. You'll know why. (If you look in the perks menu, you'll see 15X backstab damage as a perk. Now imagine 30X.) - apart from that though, they're pretty equal. As in, they have gear that kinda boost the same-ish stuff... Oh, and a certain horse makes a comeback.

-The best side-quests/ repeatable end-game missions (preferably missions that lead you to dungeons)
Thieve's Guild only and completely. db has repeatable "kill dudes" quest, thieve's guild has the better variety... pickpocketing, burglary's (houses), break-ins (shops), etc.
I encountered none, so can't answer about this one.
-The best integrated in the game (being adressed as a rookie while being the guildmaster for example of how it's not supposed to be)
Dark Brotherhood. Thieve's guild keep's addressing me with greetings like "So, you're brynjolf's new protoge?". No, I'm the guild master, perhaps you've heard of me.
I hear about DB stuff on the streets and such + the hideout, it's better.
I think DB would fit better (Legion is war, your character just generally likes to kill things?)