Was I the only one who noticed Hermione lied? ("Hey I put a memory charm on my parents!" then later on "I've never done a memory charm before but I know the theory") I kept expecting her to die or something important to come out of this but it ended without resolving it.
JKR explained later that it's a different kind of memory charm. One kind is a mere modification of forgetting some moment, the other is making people think they are someone else.
3. Why mess around with Dumbledore's past? Is there any real reason to not have a character that is actually good and not haunted by some terrible mistake they made? It's rather politically correct, in that you aren't allowed to have a pure good person or something.
This was needed to explain why Dumbledore had Harry's Cloak, and to show Dumbledore is, after all, just human.
5. Despite Ginny being only 1 year younger than Harry, she is treated as a child by everyone, universally. There isn't really an excuse for this.
To you and me, no. But remember that she's in a family where each and everyone is older than her and where she is a girl, and that everyone has seen so much suffering and death that they want nothing to happen to her.
9. Plenty of unexplained stuff. How did Umbridge get Moody's eye? etc
The Ministry got to Moody's body before Bill/Arthur Weasley did. The Death Eaters were pretty much inside the Ministry at that point and Umbridge isn't the kindest person either.
I loved reading this book, it's the only one I started reading at the point I got my hands on it, and finished within 24 hours (both OotP and HBP took me two or three days). I, too, thought the middle was extremely boring (bordering on Order of the Phoenix beginning-boring). Lots of it was predicted by fans which was of course to be expected considering everything has been predicted by fans from "Lily is a Death Eater" to "Lupin dies to Wormtail's silver hand".
There's things I can understand not liking about this book, but it is all more or less negated by the fact that I enjoyed reading it a lot. I didn't like Dobby and Hedwig dying though, both of them seemed so innocent and immune to everything evil surrounding Harry. But that's the reason they were killed off anyway.
I have to say that I was also confused by the whole Elder Wand thing, how Draco was the Master without having it, but because Harry took Draco's other wand he became the master. All confusing really. Anyway, the book was well written even though I guessed the plot twists, and I enjoyed how it explored Harry's character in even more depth then usual. I was really let down by the epilogue, it was quite lacking. I wanted to know if Harry became an Auror, and what Ron, Hermione and co do for a living.
Draco was its master because he was the one who Disarmed Dumbledore on the Lightning Struck Tower at the end of HBP. Dumbledore intended Snape to have it though. Harry did indeed become an Auror under Kingsley's share, Ron is working at the Weasley's shop with George and Hermione does something with Care for Magical Creatures at the Ministry. JKR gave it all away in an interview later, didn't put it in the books because everyone would be allowed to think their own of the series then.