There were some poor choices of scenes to keep and scenes to discard; for some reason, my husband wanted to see the logic problem with the potion bottles that Hermione solves--he claims it would make the awarding of points to her at the year-end dinner logical. I would have appreciated another scene with Snape at the end of the movie (just because I like Alan Rickman), either to explain why he was being a hard-case on Harry, or at least Dumbledore should have explained it in the infirmary [and if you're impatient, Snape and James Potter, Harry's father, detested each other as much as Harry and Malfoy do, but James did something Snape could never forgive him for--James saved Snape's life, so Snape felt he owed a payback to Harry].
At no point in the movie do we learn that Dumbledore sent the Invisibility cloak to Harry for Christmas, nor do we see Harry in the nice sweater (that's 'jumper' in British) that Mrs. Weasley knit him. It would have been nice if there were a montage of months between each of the significant scenes in the movie; remember, the book covered a whole school year, we don't actually get a sense of that on the screen. It would have been nice if Warwick Davis, who plays Professor Flitwick, didn't have as much prosthetics on his face; and it would have been nice if the Potions laboratory wasn't quite so dark (doing alchemy in the dark is not safe!).