1. Rune Display - I'm going to make an analogy to Window's view modes. Right now, Runes are displayed as large icons. It would make navigating a hundred times easier if there was an option to make it into a "List" view w/ a small picture and the name of the rune in a SINGLE line. On top of that, I don't need to see the same rune 10 times over, a simple x# would be sufficient. With those small changes you could manage almost all your runes in 1-2 pages instead of scrolling up and down for hours trying to find specific runes.
2. Mastery Pages - 3 Pages just like the rune book would be a HUGE fix to have.
Just those two small changes would make organizing a thousand times easier.