Nice breakdown post
I'm giving my 10 cents on what usually make people unhappy about the skill system
-Bow
On my current playthrough I'm at ~30 skill level, I honestly never felt impeded by draw time/stamina usage. Fair to me

-Running and Jumping
Honestly these two should be merged as "athletic" skill... when running home to haul wood or metals I find myself using the first boss buff and jumping around to level it. Jumping is such an important mechanic in this game yet you have too few occasions to level it legitimately

-Mining and Woodcutting
That one I noticed that the higher tier tool you use the more materials you get. With Bronze axe I struggled to get acorns and birch seeds. Now with Iron Axes I get them half of the time. I have no opinion on this I just noticed that today

-Death skill penalty
I think it's not THAT bad. But I know a lot of people who play survival games are, more often than not, perfectionnists and completionnists. I think a great way to balance this would be that each time you die, you can cancel the penalty by doing something within a time limit (like reaching a level 15 comfort bonus within 5min after death, or drinking a hard-to-come-by potion)