System is meant for multi-faceted progression + customization, during League's infancy, something unprecedented in MOBA.
I don't think making one better, ditch the other is going to solve anything. It is an interesting thought to move Runes to be stats only while Masteries become passives only. Runes probably need an global adjustment first though.
Not necessarily relevant to discussion
Adding complexity to and tweaking the R&M are tricky business. They've distorted balance a lot as is. You need to understand that if you removed Runes or Masteries, heck, if you made a combination system, shit would be broken everywhere.
When a champion is designed these days, you need to consider things like; would they be OP with X Rune? Y Masteries? Should this influence their range? What about base stats? Does this champion want the +2 HP regen? Do we need to compensate by lowering base HP regen?
That's just on the champion side, start getting into all the little +% you get throughout the trees and think about how those interact with items; that's when you'll realize how much of a clusterfuck all this really is.
At this point, R&M are like Flash, the game is too far gone to survive without. If there was a point where removal was possible, it is long past. If Riot continues with the current approach to balance, R&M will always be a balancing problem and one that a simple "Get rid of one" or "Take the best of both" won't fix. Too much has been affected already. Slower, systematic change is required.
Things are balanced assuming available resources don't change much. Preseason can come screw over all our precious theorycrafted customization. When that happens, best case scenario is previous balance changes aren't nullified.
