Completed my first play-through recently and one thing that really nagged me was the lack of skill bar customization. It would be AMAZING to have the option to toggle additional skill bars on screen simultaneously and not have to scroll through them one at a time. The bars could be stacked at the bottom and/or mounted to either side of the screen edge. I believe RIFT and WoW (off the top of my head) have this UI customization built-in and it would be worthwhile to make it available here. While not every build uses a ton of skills a few do and it was annoying to have to scroll around to access them.
Secondly, when updating gear, occasionally I'd lose abilities due to point shifts in different ability trees, which is fine. A suggestion would be to grey out unavailable "learned" skills in the skill book or have a toggle button to sort skills in the skill book UI for skills that can actually be slotted.