The MQ, I will agree was just as cliche. What about factions?
:D Let me try and remember.......
Morrowind mages guild: Go find some herbs!... K. Go kill some dudes that are teaching magic but not mages guild members. Go find some dwemer stuff. OMG the guild leader is a moron? Kill that fool and take his place.
Oblivion mages guild: Go fetch some stuff to get into the arcane university, you made it! Go make your staff, OH NO! Necromancers killing everybody. The guild leader is a moron!? He sacrifices himself and you take his place.
Morrowind fighters guild: I honestly don't really remember the plot other than Eldys(sp?) fire-eye being crooked and working with the camona tong.
Oblivion fighters guild: The fighters guild is getting pwnd by another faction! You gotta find out what's up with that. Oh no! That faction is totally crooked and evil. Kill them and become the leader.
Morrowind morag tong: Walk up in the place and kill people. NO real plot. Then go fetch like 30 objects
Oblivion dark brotherhood: Go kill people, but wait! A member of the brotherhood is killing other members. An assassin among assassins?
he tricks you into killing innocent people... Oh no! Cyrodiil's brother hood is basically destroyed but you kill the traitor and become the leader.
Can't speak for the thieves guild as I never finished it in Morrowind.
Edit* My point is neither game is cliche' any story can be boiled down to look terrible or cliche'