I personally think 3D is good. Yes some of the films don't need to be in 3D, but I personally enjoy it.
I do feel sorry people who have to wear polarised glasses in real life, as these are the ones who gets headaches, as the 3D glasses are also polarised. I wear glasses for long distances and I'm fine. It's just those with really bad eyesight that can't watch them.
Films like Up, Avatar, Monsters vs Aliens and Christmas Carol were amazing in 3D. I saw Shrek in 3D the other day and it was really good, looking back on it I feel I still would have enjoyed it in 2D, but I still prefer watching things in 3D as it's something you can't do at home (unless you have a few grand lol).
I'm not sure if I want to see Harry Potter in 3D though. If I have enough money at that time I might try both lol.
I agree that the formerly 2D films converted to 3D are rubbish though - I saw Toy Story 2 in 3D and the 3D wasn't that great, and the glasses were uncomfortable (this was at the 02 Grenwich. Read 3D glasses are so much better)