Probably has something to do with the archaic adobe client that Riot refuses to change/update.
Things like greying out the background and disabling features during ques are most likely too deep in the code to undo. It only continues to exist because rebuilding the framework for the UI would be time consuming. For as popular as League is, it's amazing how dysfunctional their primary UI is.
As for the runes, that is because people spend money for a feature that many competing games give for free. Riot is basically monopolizing on your convenience by making it impact the game. I'm surprised there isn't more outrage over this. The whole system of talents and runes could easily be combined in a content patch and solve many complaints and issues, as Blizzard did in HOTS/WoW.