I love act 2. The creepy horror feeling everywhere. Especially the abandoned village is great. And of course Jaheira, she is the best .
Act 3 started out nice too. I just reached the lower city.
I like a lot of the things about Act II, including the dark, creepy feeling that you mention.
The only things that stand out as "weak" points to me (in my opinion) are:
1. Not enough Ketheric. I wanted to talk to him more.
2. I hate to say it, but I just didn't care about Thaniel. It was more of a hoop to jump through than something that captured me.
3. I just stumbled across certain NPCs, like the large drunk and the toll collector. Would have preferred some lead up, some commentary about them and their history. Maybe that's in Act II somewhere, but I didn't notice it.