1. I like the Short Rest passes time idea.
Depending on how it's implemented, it could make you have to think more before using a Short Rest.
Having different encounters would be interesting as well.
I think that a day/night cycle without that would work too, however, and I'd rather have Short Rests be less limited than they are right now.
2. Multi-select and auto-search with filters are very needed.
I don't like the idea of not being able to use auto-search more than once though, since it's a convenience feature like highlights.
In addition to these, I'd like a feature to automatically add certain items to wares, and wares to be in a different menu.
4. Yeah, the HUD seems very cluttered at the moment.
I'd like to see a way to collapse menus (like the message log) and customize their existence and placement.
6. I think that food should be able to be converted into Supply Packs (anything left over is stored for the next conversion), maybe automatically.
Short Rests shouldn't have a limit, but food could be used to give bonuses to Short Rests.
14. This and transmogrification.