I hope there is no Thieves Guild, no Mages Guild and no Fighters' Guild in Skyrim. My guess is that at least there will be no Mage's Guild, but the factions of Synod and the College of Whispers in its place.
The generic "join a guild and get some training" thing is boring. I'm really hoping for lots of different factions, with different names, histories, etc., potentially in conflict with each other. I don't want to hear that "The Fighter's Guild is hiring today" etc. I agree with the OP, the Thieves' Guild was too nice to everybody. I hope there will be some faction that will fence stolen goods without caring whether you killed a guard (who should be an enemy of the Thieves' Guild).
In my view, the Dark Brotherhood was not the "Assassin's Guild," in that generic guild sense. Rather, they were a in interesting faction with a particular group of NPCs, backstory, and one of the most well-written quests of any RPG I have ever played (Whodunit?). I'm hoping for lots more factions in this vein.
I've liked them since their implementation in
Daggerfall. What bugged me, though, was the "Competion" aspects. As long as there are Sabre-toothed tigers getting into Wealthy Peoples homes, as long as aliens and monsters and brigands roam the countrysides and hassle people who'd pay to make them disappear, as long as rats live in paying people's basemants, and as long as there are people willing to kick ass for money, the Fighter's Guild will be around. They're a combination of Exterminators (of varying degrees of professionalism) and PMCs, moreso on the first than the second. I wouldn't mind them having morally-ambiguous contracts now that the empire's fallen apart and can't regulate them (But not Assassinations).
There will be Thieve's guilds as long as there are thieves with a sense of camadarie (The khajiit would easily start such things, due to their culture's endorsemant of such activities, members of other races perpetuate it). I see them as on some levels just an "Urban Bandit Gang", looking out for each other as they exist on the wrong side of the law on the inside of the walls, while the individual members pursue their own illegal schemes, endorsed and encouraged by the other members.