Crazy idea: Cut the number of runes in half and make them more interesting and significant
90% of the current runes are a bunch of nickel and diming garbage that just add or subtract damage on you. But they have to be that way because you have to pick 6 out of the 49 total among all the different trees.
Name one thing that has 49 distinct varieties that don't overlap all over the place. Go ahead, I'll wait. There's about 12 human detectable colors and the rest are all derived from variations in their saturation. There's 10 unique digits in our base 10 counting system. There's 12 pitches in the commonly used equal temperament division scheme (humans can detect more but only a small percentage of people can in a meaningful way and usually requires training).
You can't justify to me that 49 is the right number of runes. Tons of overlap. No significant choices. "Scorch: Your next ability hit sets champions on fire dealing 20 - 60 (based on level) bonus magic damage after 1 second." Hats off to the design team on that one. Creativity and significance out the wazoo.
Simplify. Reduce. Of the ones left, increase their power in a non-directly damaging way. Make the choices less directly quantifiable. That will make them less of a braindead process and more of an X-factor that players can use in creative ways. There's nothing a player can do creatively with "I do 20 - 60 more damage now." That is shitty design. Evolve.
EDIT
I also think along with reducing the total number of runes that reducing the amount you pick from 6 to 3 would go a long way. If you estimate that runes account for around 30% of a champion's power in a given game then that means each rune can have about 10% power, or 1 at 15% with 2 at 7.5%, etc. With 6 you get something like 8% for a keystone and 4% for the lesser runes. That's unsatisfying IMO, hard to track in game what those 4% are really getting you, and a feelsbad experience all around.