I think that runes reforged has a number of problems including that many runes are far too optimized for certain champs and not nearly enough for others.
On many champions you just take whatever is closest to what you want rather than what's optimal.
For example, all this time later we STILL have no way to get magic penetration or lethality from runes without having a dash. For some reason having a dash or invisibility for sudden impact is rewarded by having even more damage.
However, why would the game be more fun without ANY runes/masteries whatsoever? I think they add a nice amount of flavor to the game. I've played HotS where they ran a talent system and it wasn't nearly as much fun. Especially because most of the talents were random nonsense unless you were going for a niche build which was rarely better than just going the regular stuff everyone always used.