Crawling: Love the idea and the animation for it is great. Perhaps keep it in but make the places (in the ship at any rate) shorter, so you're not crawling for what feels like eternity. I think that would tidy it up a bit. Maybe have a scene where you need to run away from some.. most likely, tentacled monster which includes crawling in order to escape. Not escaping results in amusement for all.(or, if you like, a chance to escape and carry on running)
Exploration: I think a simple fix to all your problems, and our frustrations. A map. Probably open/close type would be best as I like the size of the screen as it is.
Boss fight: It is hard but amusing. Possibly too much health, yes and the rest of your suggestions sound intriguing so I'd like to see how that goes first.
Invincible Escapes: Keep it as it is. It's fine (I do use the warrior type weapons though) Not sure how magic users feel ...
..It's nice to have game's actually trying to be hard!
no pun intended.
Game Speed: Whatever I'm playing atm 10Dec/1am GMT is perfectly fine.
Arrow: using Krystal - no problems at all. Great Balance. Good Job #thumbs up#
Character Balance: Couldn't say at this point. only using Krystal
Levelling: Not sure I'm keen on the idea. Depends on the implementation. I love RPG elements usually. Just not sure in this. See what you've got :p