Save for maybe summoner spells because of how ingrained they are at this point.
Despite all the love (read: Rose-tinted goggles) of old runes, they never really solved anything nor allowed for unique playstyles. There was a "right" rune page in almost every situation save for the person who is going to bring up some gimmick page that worked in 1/1000 of matches due to a very specific lane/champion fight.
The same goes for new runes: Yes, you still have the ability to do some gimmick/unique playstyles but 90% of the time there is a "right" rune page to go for a champion. Granted the results of a bad runepage aren't as detrimental as before but going in with a bad runepage is still a detriment. And of course everyone will want to address how runes/masteries have always tilted balance. See: Massive stat buffs they had to give to every champ after removing old runes. Runes causing odd things to pop up, then they get nerfed after the champ is nerfed blah blah blah. Granted new runes still allow for unique playstyles better than old runes but this is like saying you only cut off your hand instead of your entire arm.
None of these pregame systems promote uniqueness, "choose your playstyle" or make balance easier. Every champion from Season 0 to now has had problems because of the rune pages. Yes, even the old ones where if you didn't have AS reds you were literally unable to jungle.
Honestly? Removing EVERYTHING is the right call. You cut down tertiary factors and make the game easier to balance because there's less to manage. Yeah, you lose balance tuning levers but at the same time you also help reduce frustrating situations where you miss the mark because you should have nerfed a rune/champ when the opposite was true. You also cut down on player frustration because now you can't load in at a massive disadvantage or with the wrong page or otherwise.
If the game is only balanced around the champ you bring in, things will be clearer and players won't be as frustrated.