A lot of the issues would be solved by just increasing the rate you get skills up.
Most of the list is helped by better skills and I think it is a good way to fine tune the changes made.

Personally I would like to see a wider variety that offers more choice including middle ground stuff. I think increasing number of foods that can be eaten or introducing more middle ground foods would help that.

Also the restriction due to more items causing more back and forth for inventory emptying could be solved by increased inventory slots.

I do like the concept of making food choices but it feels to me the rest of the game mechanics need to be adjusted to that.