That was my reaction, too. Having tailored upgrades/sidegrades to each champion's abilities so that you can tune them to your playstyle would be a lot easier to balance and downright cooler than the rune system.
There are 137 champions in League.
Each champion has four abilities. If each ability had three different augments (damage, sustain, utility), then that's 1644 different augments that would need to be made.
Now, that sounds like a lot, but I think it's a much less of a huge effort than it seems.
From a coding perspective, each one would be about as easy to code as a simple item, since all they would offer is altered numbers. Increase a slow duration here, convert a stun into a knockup there, add more scaling on this ability, etc. There wouldn't need to be any unique effects added.
Artwise, they could simply recolor the ability icon that is being modified (e.g., red for damage, blue for sustain, yellow for utility).
It would be a daunting task, but it would certainly be possible. It would allow the devs to fine-tune the different options a champion can have. No more "We can't buff this rune because it would make the champs it's actually good on overpowered" nonsense. Each champion would be their own entity, and their abilities could be tuned as such.
Does Jhin have too much movement speed? Gate a portion of it behind an augment. Force him to choose between it a different upgrade to his kit in order to become The Fast.
Is it hard to find a balance between Zoe's viability and fun-police abilities? Give her the choice between being more control mage-y with traps and sleeps, or being an artillery assassin-y with intense damage and range. She doesn't get both at the same time, but both playstyles are important to Zoe.
Players could adapt their champions to the matchup they are in and their preferred playstyle. You could choose defensive variations of your abilities if you're going into a hard matchup, or take augments that let you push the advantage you know you'll have in lane.
This sort of thing would add the depth that Runes Reforged was supposed to add, not set-in-stone "best build" for virtually every situation, but real choices for every champion.