Runes are the last TRUE form of customization
As a Jungle main, right now you can offset a champion's bad early game with extra AD/AP + Armor so you can clear quicker/healthier. Conversely, you can sacrifice early clears for things like scaling stats or more movement speed.
If/when the Rune system gets reworked, Riot may as well bind Runes & Masteries to champions like a passive because there will be 'the best page' and 'trash' with nothing in between.
Every champion in the game will need to be re-balanced with the Rune Update (base AD, AS, Movement Speed), and Runes will be one more thing for Riot to target when nerfing them.