Okay so I'm not advocating for a return to the old rune system, but simply putting forward an idea of being able to choose whether the armor or MR you get from runes is flat or scaling.
You're playing a melee top laner and the enemy picked teemo? Double flat MR runes to survive early game. You're playing adc and they have a rengar and a talon? Double armor scaling runes that are weak in laning phase but stronger later. To me, it seems relatively simple and easy to implement, and I can't really think of a downside. What do y'all think?