I loved the way Snape's memories were done, and it was a nice montage, but I also noticed that there were scenes that couldn't have been Snape's memories included. I also felt the Hogwarts portion was a bit too abrupt - and it also gave the impression that Lily fell for James right away, which was far from the case. The memories that were included were handled well, imo, but they should have put in a little bit more.
I found the ending kind of random and weird. I don't mean the epilogue, which I actually liked better in the movie, as the whole weird "Harry's kids, despite obviously being involved with the wizarding world, are apparently completely unaware that their father is the most famous wizard in the world" thing in the book made me nuts. I just really didn't like the way Harry explained about the elder wand to Ron & Hermione, not to Voldemort, or the "we're just going to stand here and stare" ending with the trio.
I didn't like the way Fred's death was handled at all. If someone was watching who hadn't read the books and didn't know the major plot points from just living in the Western world (okay - not that likely, I'll admit), I'm not sure they'd even fully realize he was gone. It wasn't completely invisible, but it wasn't clear enough, imo.
The duel between Molly and Bellatrix was pretty cool, but a little too abbreviated, imo.
I agree about Lupin and Tonks. They were almost non-entities and there wasn't enough story about their relationship or the baby. Their deaths seemed almost irrelevant, as if they were just two more random Hogwarts students lying on the floor.
I have mixed feelings about the changes within Hogwarts (Harry appearing publicly before trying for the diadem, not seeing all the people showing up in the Room of Requirement, etc.). I was also bugged by Hagrid's role in the movie. I honestly didn't like the way Rowling handled Hagrid in the later books, anyway, but his appearance in the movie was lame. There was no sign of him before Harry surrendered himself to Voldemort, and then he basically carried Harry in and vanished, except for one brief (and awkward) looking hug near the end. It just didn't work for me.
I was disappointed in Harry's duel with Voldemort. I saw it in 2D and feel that a lot of the duel was set up to maximize the 3D version (all the swooping and soaring and such). It just didn't work for me. And, as I mentioned above, I didn't like that the explanation about the Elder Wand happened later. I liked the way it played in the book a lot better.
Overall, I did like it, and it was certainly a big improvement over many of the movies in the series. But, there were definitely some aspects that I disliked. And, I hate that Harry didn't repair his original wand with the Elder Wand. Harry grew up a lot over the course of the books, and there was so much progression from a child to a near-adult that it bothered me that one of the few signifcant "full circle" elements of the book was taken away. I also disliked the omission of the cheering portraits fo the headmasters, although ds1 (he and I went together) did point out that the portraits really hadn't played much of a role in the previous movies, so that scene may have felt a bit tacked on.
Oh - and I totally missed the house elves and centaurs, and even Gwarp, in the final battle.