The cuts I'm happiest about are the "poor Tom Riddle" flashbacks. Building a case that an abused child will inevitably become a mass-murderer is a poor companion to the other parts of the series that defend the power of people to choose to do good.
Now if they'd cut Luna's scenes, that would've hurt. I could've done with less Ron, but it's not his fault he's being used as the foil to show how much Harry is maturing.
Discussing the movie afterward we decided that most plot holes can be explained as symptoms of Dumbledore's overwhelming arrogance.
People are still telling Harry not to say Voldemort's name with no explanation. The reason came out in book 7 (Voldie can spy on people who use his name), long after it would've been useful for Harry to know. Heck, if Harry had known earlier he could've suggested making "Voldemort" the standard greeting in the wizarding world. Just go down the hall saying "Voldemort, Patil! Voldemort, Harry. Voldemort, Bill." Then get to the classroom to hear "Voldemort, class" followed by a chorus of "Voldemort, Professor." The evil SOB would be driven more crazy than he already is. Yes, I'm proposing a magical DDOS attack.
Hermione is showing another aspect of Dumbledore's line "It is our choices, Harry that show us what we truly are, far more than our abilities." She's showing that she doesn't value brains nearly as much as bravery. It's just that the cards she has to play are all "smarts" rather than athletic skill or charisma. I'm reminded of the Mercedes Lackey filk "The Archivist," who also wanted to use his smarts to become a hero's companion but lacked Hermione's luck. Just as Harry chose not to be a Slytherin, Hermione chose to not be a Ravenclaw.
Not that you'd care about the distinction from watching this movie. The book showed the importance of House rivalries dwindling in the face of major threats. The movie skipped them completely. They had clues for those who knew how to look--banners, uniforms, body language--but I don't think any house name was mentioned onscreen.