I've updated the tileset. Mainly the tree texture, but it still seems wrong to me. Help greatly appreciated with that tree.
problem #1 with your tree is that your texture has a strong "vertical" look. E.g. things are highly vertically-aligned in the texture pattern, which is fair for the trunk, but do not fit roots and branches.
#2, your transition between non-shaded and shaded part of the tree is very straight, and (again) follows a vertical line, reinforcing the feeling that the tree must have a sharp, vertical edge there.
#3, roots and branches are usually shapes of their own (cylinder-likes) and thus have their own highlight and shadows.
So far, my best suggestion for you would be to re-start a new tree shape without texture (add it later), with 3 or 4 colours and focussing only on shaded and highlighted areas. I once collected trees of various video-games
on my blog, maybe it could be helpful for you ...