Should we even have masteries or runes?
Take a moment to really think about it:
Do you actually diversify things when you make a rune page or mastery page? Probably not. You look up the "right" build on some build website (Champion.gg or lolking or, if you're missing part of your brain, mobafire) and just copy that. It's the same thing with, say, World of Warcraft: Yes you have these giant talent trees with the abilities and all these neat skills...but then you look up which skills are optimal and you always get the 6 good options and the 1 flex option.
And no, this isn't something new. Reverting the mastery system won't change anything and making runes free won't either. You're going to have optimal paths that are the "right" outcome when it comes to your build.
You know another game that has talent trees? Heroes of the Storm (and technically DOTA2 now). Do you know that there's a "right" way to build most characters? Again, you probably do.
League is a game with tons of balancing levers and tools. Items, abilities, base stats, etc etc etc. Why do we need yet another false customization tool that is locked off for new players? Why do we need any sort of talent tree, old or new, when the game already has enough complexity? Why do we still pretend that any sort of choice we make in these runes or trees (old or new) is customizing our playstyle our way and not just making a subpar choice?
Will it be easy? No. Not at all. Removing these after balancing the entire game around both these subtools would be painful. Champs would plummet in win-rate while others rise up to be gods. You'd need to retool every champion's base stats to better fit the game, both in terms of level 1 and a per-level basis. But, at the end of the day, it would make for a much healthier game and remove a lot of the problems people have with these systems. (Side note: Remember that time there was a bug in Season 2/3 or so when you could sell your runes for an insta-1k gold or so? Pepperidge Farms Remembers.)
Both these systems hurt more than they help. So maybe it's time we retire these archaic systems from an age where we wanted customization but could never reach it.