These changes all make the interface better without sacrificing any of the existing features or benefits.
1. 7 hot-keys and a favorites menu
Currently there are only two hotkeys (D-pad left and right), and the favorites menu can be accessed with D-pad up or down. Instead, you could have D-pad up be the favorites menu, and the other 7 directions (this includes diagonals) be used for hot keys. Alternatively, you could have both up and down be the favorites menu, in case you want to satisfy people that have gotten used to either way, but have the remaining six directions be used as hot keys.
2. A quick way to back out of a skill on the skill menu
Instead of repeatedly pulling back to get out of a particular skill tree, why not have the X button pull my view out to show all skills?
3. Turn book pages with triggers
When reading some of the longer books, I set the controller down at my side. It is much easier to turn the page using right trigger than using the control stick when I do this. Why not let us turn pages with triggers in addition to using the control stick as an option? In fact, if you happen to be reading a book while it is in a container, you can still use triggers. Why can't I do this anywhere else?
4. Map filters
Pressing RB or LB on the map screen could pull up filters. Then I could select to show only cities, or only show dungeons that I haven't cleared, or don't show places I've already visited, or whatever combination I want.
5. Categories for containers in homes
Containers in the wild don't have much use for categories, which I imagine is why containers in general don't have them, but it would be nice if containers in my home could have their items grouped.
6. Use the same button for putting items into containers as for pulling them out
Press X to put in container. Press A to take out. If you mix it up, you accidentally eat your nirnroot (reload your last save), or you emptied the entire chest into your inventory (either sort it all back out, or reload your last save). I'm up to 30 hours of play time, and I still haven't gotten used to this button swapping. The screens for looking in a container vs in my own inventory aren't any different, so it's hard for the brain to register that the controls are different, leading to frequent mistakes.
Bethesda, these are all fairly simple to patch in. You've made a game so great that my only complaints so far are with little UI things -- but why not make those UI complaints disappear?