Oh of COURSE the Main Story is important. When i played Morrowind, i was clueless, and i eventually learned how to play, ONCE in awhile i would hear about the Nevarine but i didnt make miuch of it....and it was only when i got strong that i began doing the Main Storyline
Finally i began to realize....Wait...I'm the Neravar?
For me, that was the coolest thing.
If this had happened to me brother, I know I wouldnt be apathetic to the MQ in general. Hell, what you describe is the kind of experience I long for in video games.
UBER BIOSHOCK
SPOILERS AHEAD!
I remember in Bioshock how the big reveal toward the end made my jaw literally drop, never had a game so blatantly rubbed in my face, the fact that my actions were meaningless, that all you are doing is following the whim of someone else(Atlas aka the developers) while pretending you are making the choices yourself. This revelation is taken to the limit by taking away your ability to control your character at all, while I sat there in horror as my avatar slaughters someone whom I no longer wish dead due to me NOW KNOWING THE TRUTH! I will always treasure that moment. http://www.youtube.com/watch?v=bncxTilQKAs