In spite of the game being harder to balance due to the runes. they make the game more fun and interesting. In a certain way, more diversified too. For example, I can choose to have more sustain and a safer lane phase on Kassadin with Fleet Footwork; or I can pick Dark Harvest if I want to sacrifice every chance I had at the early game for an even crazier late game. OR, I can pick Grasp against certain melee matchups.
I can pick Aerys for even better early game lane bullying potential on Pantheon. Or I can pick Electrocute for a better burst mid and late game. OR I can pick Aftershock, so that I can have a safer late game and transition to a bruiser/tank build which is arguably more useful late game.
I can pick Hail of Blades for strong early game trading potential on Vayne. Or I can pick Fleet Footwork for a safer early game. Or I can pick Lethal Tempo if I want to bet on a powerful late game. In fact, on most ADCs I can choose between Fleet Footwork or Lethal Tempo, depending from whether I want early safety or late power.
THe point is, without the runes, this game would be more boring. Yes, runes make the game harder to balance and create some crazy situations (such as Jhin with Hail of Blades in the past) - and we had some examples of exceedingly powerful runes such as Conqueror and Dark Harvest. Ultimately, I think this is a worth trade off to have a more interesting and fun game. It feels good to have the choice of using things that may help my champion have more power during the game; without that, the game would not be nearly as fun. Especially since some off-meta builds are only possible thanks to runes (ex: full AP Lulu with Electrocute/Dark Harvest).
Of course, runes could be better designed. There are way too many damage oriented runes, and not enough defensive/utility options in the paths. Some keystones more or less do the same thing, and are usually picked based on which option is the strongest in the patch (I am thinking mainly of Electrocute/Dark Harvest/Aerys/Arcane Comet, but another example of this is Hail of Blades x Press the Attack). Some runes are designed in such a way they end up giving champion powers they would not have otherwise (such as Conqueror/Ravenous Hunter giving sustain to champíons that would otherwise have no sustain, or Aftershock giving tankyness to champions that would otherwise be squishy). Finally, some runes are forgotten, they are very weak or too situtional to be used most of time (some of them used to be strong options, but have been nerfed to obscurity): examples of such runes are Scorch, Celerity, Unflinching, Last Stand, Hextech Flashtraption, Shield Bash, Time Warp Tonic, etc.
I am pretty sure Riot can, and will, solve those issues over time. I welcome runes, for they are a great addition to this game. Most of time, when people complain that runes should be removed, they are mainly thinking of how runes make the game hard to balance. This isn't a lie. However, I think there are so many worse issues than the runes, and many other things that make the game hard to balance. Runes have the potential to be a great addition to the game if Riot manages to balance them properly.