As far as the paper making skill is concerned, it seems like what exists right now is just a placeholder for future content. The fabrication of deeds, physical paper ballots (in game) for voting, using paper to make books (including skill books), and perhaps other things like origami for more decorative items certainly seems like a possibility. The devs certainly seem like they've had various plans for paper that at the moment don't seem to be implemented and some failed experiments in the past that they may want to get into in the future. If it has those separate uses, its appearance as a separate skill distinct from other carpenter skills makes sense. In its current state though, I agree that it does far too little to be justified.
Inventory management is something that while it looks bad, compared to what was around in the past the current system is a huge improvement. I wish there was more consistency between storage compartments, particularly with stockpiles and carts in terms of the number of items contained in each "slot". Breaking up dirt and sand into groups of 5 and then being forced to recombine them when pulling them out of storage seems to be far too much work. A much larger problem that I find though is when you get too many storage containers in one spot, there is a huge lag on both the server and on the client. That in general it needs some attention and TLC I would agree.
There are more things I could add here, but like you pointed out this is a comprehensive list of things you've found and have irritated you in terms of your gameplay. Much of it I even agree with, so thank you for making this post.