I played the first Halo and played through it, acknowledging it for what it was; a way to pass time until I found a game I could really delve into. In that role it was entertaining. I really started disliking Halo when I started reading articles and ravings by people claiming the Master Chief was one of the best characters created in a video game, rivaling Solid Snake in complexity or Crono in ingenuity (Those characters who do not speak, so through the course of the game you make their own persona). The Master Chief is neither of these things. He is a generic badass, placed in game to give you an excuse to kill the badguys.
The OP's idea that the story is there as filler or just as a necessity that they banged out for the game is something that I would really like to agree with, except that they've published entire books attempting to make the story something compelling. Aside from the obvious argument 'I shouldn't have to read some half baked books to make the story of a game complete' I feel they in some way undermine the OP's argument. Otherwise I have no trouble agreeing with that part of the OP's write up.
As someone who plays most of his games to appreciate a good story I was willing to let this one slide by with a nod and an acknowledgment of a job decently done for what it was, until people claimed it was something it was not.
EDIT: Bioshock's story was awesome haha