Excellent observations. I've got about 20+ hours in and I'm loving it, but would agree with most of the points above. I've not left the copper age yet, but I'm getting there. I've been playing MC for years and TFC is still my favorite mod.
I love the clay molding feature. I find that it makes the game very immersive and I enjoy it even if it can be a bit repetitive.
I completely agree on the wolves issue. I tried hunting them all, but they do come back and it's pointless. If you're in the middle of something and a wolf attacks, you're generally done at that point. With TFC, you had a feature that the longer you stayed in an area, the less likely mobs would spawn. Maybe something along those lines would work.
Farming and tree maturity are right on point in my opinion. This may be another thing I'm missing, but I'd love to know how to get more saplings when cutting down a tree. I hate the deforested look around my house. I do agree with the multiple stages for look, but otherwise, I think it works as it is.
I don't know if I'm just missing it, but some sort of armor really needs to be a necessity. Even something as simple as reed pants or shirt would be helpful. As it is, my combat involves a 2 high dirt pillar as my main mode of defense.
Again, I am really loving this game as it truly is the kind of survival game play I've been looking for. Keep up the good work!