I've found one of the major factors in being disappointed about (or ruining completely) a game is when you expect it to be something that it is not.
I think this is why I like some games that others don't. I've heard lots of grief, for instance, about Halo 3 not living up to expectations. Well, I think part of that was the fault of the gaming community for placing those expectations too high (though the relentless over-hyping certainly didn't help). I found Halo 3 to be a satisfying and fun end to the Halo trilogy, not disappointing at all.
As previously stated, SSBB is a fighting game. Whether it was the intent of the developer or not, I never expected a very deep story out of Subspace Emissary. I still found the mode fun, even if the last level was tedious.
Elaborate stories belong in the genres they are suited for. Fighting games is not one of them. Fighting games are about beating the crap out of your opponent. Subspace Emissary delivered plenty on that count.