As it stands, Runes have a few problems with them.

While I could talk about how X rune is incredibly meta defining and such, I'd like to go out on a whim and say that something about the rune system as a whole.

1. I have no idea what runes my opponents or allies are running outside of their keystone.
2. Some runes crowd each other out (Celerity/Waterwalking).
3. All runes come out at laning phase (except for certain stat bonuses and predator).

I thought of an updated system that will at least try to mitigate these three problems, which involves taking 3 keystones instead of only one. These three keystones come online at levels 1, 6 and 11. Keystones are separated into 3 tiers, Tier 3 being allowed only at your third (level 11) slot, Tier 2 being allowed in either your second or third slot and Tier 1 runes can be put in any slot.

For example, Bone Plating could be a Tier 1 rune, where you simply want to survive in laning phase, but you might be losing out on something like Conqueror which would give melees a lot more damage. Tier 2 runes could be something like Predator, which allows you to roam much faster, but you might lose out on something like Aftershock which generally warps tank matchups a bit too much. Tier 3 could be incredibly powerful burst runes such as Comet or Electrocute, to provide those additional sources of damage to punch through a squishy, or Hail of Blades to get more attacks out faster.

It could use some tweaking and I really have no idea as to the meta connotations, but I think this system might provide slightly more variety compared to the system we have currently.