Few small things I've noticed:
- Disarm Traps (tier 2) is available at tier 1
- Charm completion bonuses have pet bonuses, but they don't display when you socket them, not sure if you were aware
- I think one skill isn't visually connected to its tree, I don't recall which one, I'll try to recheck and edit this later
- Nature's skill tree seems to be lacking 2 skills, what are you planning to add?
I like the MI set idea and the AoE stun you gave to bats, as well as changing the quest monsters (drowned sailors)