I know Runes Reforged has sat poorly with a fair few people and been nothing short of a balance nightmare for good ol' Rito Gams, but let's not pretend the old runes system was any better. Maybe balance-wise, I guess, since there were only a few actually worth taking; AD, AP, AS, Armor, and MR. If you were feeling spicy on your tank pages, you could run HP reds, or mages MIGHT run CDR blues, but the dominant was AD/AP Quint, something offense for red (I think mages took M. Pen reds, anyone AD took AD reds), armor yellows, and MR blues. Variety was scarce in those rune pages, and they were also giant IP traps.
With the new runes, you have constant abuse cases coming up; Ryze with Conquerer and Ravenous 1v5ing people with stupid amounts of drain-tank, Cassiopeia and Conquerer, pre-nerf Aery, DH, Fleet Footwork, the ever so "beloved" Kleptomancy (I loved that keystone, I still miss it), every ADC running Inspiration secondary for Total Biscuits and Magical Footwear (which is a good 400+ gold of free stuff during lane) and the list goes on. There just doesn't seem to be a way to keep Runes Reforged runes in balance.
With that in mind, what if these systems were removed entirely? No more WoW-like skill trees, no more keystones, no more pre-game stat boosts, nothing. Just the champion, their stats, and the items they can buy. It would expose a lot more problems within the system as things are currently, yes, but I think it's easier to tweak base stats without having to worry about keystone abuse than it is to try and compare the same champion with every possible combination of runes or masteries to see which are most abused or need love.
Just my two cents, though.