Just watched the entire series a month ago with my Dad (who really loved it) and I didn't care for movie as much as I did when I saw it at the theatre. It felt off. As has been pointed out, Alliance ships looked different, Simon was VERY different, didn't care for the explanation of Rivers mental state, the Reaver explanation didn't hold water (as has been pointed out), cargo bay lights were too "sci-fi movie" looking instead of the normal warmer lights.
It was like watching an alt-universe version of Firefly. It's just really noticeable watching it back to back.