The game would be much easier to balance by just removing runes completely.
Some runes just end up getting abused and many champs just end up having a "best" rune page that people take every game.
The game would also be easier to balance if items were removed completely. There are often cases of champs abusing items meant for other classes. Mages abuse support items, marksmen abuse bruiser items, Ezreal abuses every item, the list goes on.
Even further the game would be easier to balance if champ select were removed completely. Too often there are some champions that are picked every game while others are left at the bottom. Some just end up nerfed because of pros at the expense of the average player. If everyone just played the same single champion every game it would guarantee a balanced game.
But this game is starting to sound a lot more boring isn't it?
If pure balance were Riot's #1 goal this game would've been balanced years ago. But the fact is that the more choices you give players, the harder it is to balance those choices. But those choices are a huge part of what makes this game fun. Now not everyone has to agree that runes are the best system, but let's not use balance as the only argument against them. I would argue that items present the same balance issues runes do, but I've never seen anyone ask that items be removed from the game completely. Because players like choice.
Even if some rune build is considered meta, that doesn't mean it's the only one you can use. In fact I often see the same champs take a variety of runes. I've seen 
players often take Fleet Footwork or Arcane Comet to compliment how they want to play/build. Just today my team was beaten by a 
running Predator. I've seen some people say gathering storm is useless, and others say that it's overpowered. Most people take Arcane Comet on 
, but that doesn't stop me from playing him with Unsealed Spellbook.
It may be true that some of these builds are simply wrong or less effective than others. However that doesn't mean we should get rid of the option to choose completely. We should also consider that meta builds matter significantly less in lower mmr games. I've often heard people say that you can carry with anything in bronze. If that's the case why ruin the fun of lower games just for slightly better balance at the top tiers of play?
Even if runes were removed completely we would still have top tier players picking the same things every game. Champs might be balanced based on the same rune page every game, but removing runes would still leave us with champs forced to play one way.
Of course game balance is important, but at the end of the day a balanced game needs to take a back seat to a fun game.
tldr; runes are less balanced but they're fun so it's k
