Don't want to spoil so I won't go into the main chars personality/reasons but I see where you're coming from. Some choices/reactions just make him seem like a villain through and through but this should change with time.
Just the other day I lowered the chances of chests being empty as well as added gold to them. Them being empty should be a rare occurrence now, hopefully. About the doors that lead straight into a wall, it's things like this that you just forget....Sigh. Walking on roofs??? Jesus, will look into that.
No crafting though, I guess you got that from the fact that you get misc items like "berries" and such but no, no crafting. The list of droppable items is quite short which is why they're there. I will take another look and see if I can add something else...maybe "trinkets" that can be sold for gold. i.e "broken pocket watch" and "jewelry" to name a few.
As for the spells, I was going for more of a "surprise happening" type of thing. Their strength, on the other hand, is quite noticeable so I left it at that. Each upgrade is considerably more powerful than its predecessor.