Your post almost exactly mirrors the one I made when I re-watched the movie a few months back. I mean, it had some clunkers (see the aforementioned Jesus, half-human, Eye of Harmony, etc.) but I think what people couldn't get behind at the time was that it was a different way of telling a Doctor Who story and (surprise!) the storytelling in the movie is much closer to what we've seen in the current series. In fact, in some ways, what people hated about the Eighth Doctor became part and parcel of Nine and Ten.

Regardless, I ♥ me some McGann. Also, Fitz. I am overdue for some EDA goodness....