I think the subplot of Ron and Hermione's bickering being left out was very big, it wasn't just about the Firebolt, it was also about Scabbers and Crookshanks, which was very briefly touched on. It was major in the book though, plus it would've been the first big fight they had, I totally forgot about Scabbers and Crookshanks and also Buckbeak's fate in the movie because there was no focus on it. I do think the tone of the third was good, but wish they could've been more faithful.
Are you just talking about the third? 15-20 more minutes, more time spent on Buckbeak's fate, the conflict with Ron and Hermione regarding Scabbers and Crookshanks and most importantly more time spent in the Shrieking Shack explaining the Maradur's past. Only reason the movie didn't get a longer runtime though was the Matrix sequels, WB got very gunshy about long movies after those movies underperformed so much and stupidly thought it was the runtime, not that the movies just weren't entertaining. If you want what should've been left in 4 and 5, that'll be a much longer post.
It differentiate how dark and light magic was different though because the Order did the same cloud thing, only as white instead of black. It was a horrible change and completely changes how apparation is explained in the books.
It's the same director who did Order of the Phoenix though and he's showing the same disregard for the books, once again talking about the romance of the movie, instead of what should be the central theme, the Origin of Voldemort. He's cutting out the very heart and most important part of the book. You can cut out the Ron and Lavender and Harry and Ginny subplots entirely and it wouldn't make a bit of difference. Also the movie being rated PG when it's a movie about basically open warfare in the wizarding world and you have two big plot points involving nasty wounds, Harry using Sectumsempra on Draco and Bill getting attacked by Fenrir, although Bill probably isn't in the movie anyway and apparently the Death Eaters attack on Hogwarts is cut down big time, replaced with an attack on the Burrow, that doesn't make sense, since it's supposed to have major magical protection since Harry spends summer and Christmas there.