Saw it last night with my daughter, and I concur with your analysis. Hermione was much better than Harry or Ron, and much more convincing.
I also found a number of things that just didn't seem... logical. Without going into spoilerish details, how could the ministry not be able to stop three junior wizards from leaving? And there was one character who showed up that I thought was killed off in a previous movie... and who I had hoped never to see again.
I agree on the shaky running scenes... too much movement. But at least in the movie, I could follow the reasons for the various changes of scenery. In the book, that was too hard to follow. I think the fact that they made every new place completely different - climate, season, surroundings - made it easier to follow.
My biggest regret... I don't have a time-spinner to go forward to July, for part 2
I do feel I need to reread the book now... if only to see where things were different.