I never had a problem with SMS's soundtrack. I liked the choice of instruments. It suffered extensively from single-theme syndrome though. Super Mario 64 did too, but the different versions of the single piece of music in the game were more cleverly done.
As for SMS itself, I enjoyed it. Aside from the utterly stupid Boo redesigns.
QFT completely (in addition to the SMW reference). That sort of thing really bugs me. I mean, hey, I know it's not fair to expect Koji Kondo, or whoever, to make up tons of new songs for every game, but hearing the same tune remixed in every level makes it seem... I don't know, small, or cheap, or something. It's not a game-ruining thing, but I'm obsessive like that (NSMB's theme being a remix of SMW's credits was kind of a turn-off, though).