What if some more runes had defensive mechanics?
I think it would help with the damage issue a lot because first, we'd have more options to get a little more durable without being an aftershock user, and second because it would shift usage away from higher damage runes.
Here are some ideas. All are in addition to current effects unless stated otherwise.
Precision
Last Stand: Gain half of the damage increase value as damage reduction (2.5% - 5.5%)
Domination
Taste of Blood: Now also increases armor and MR by a flat amount for a few seconds.
Sorcery
Phase Rush: Take reduced damage from the target you triggered this on. Half effect vs other champions.
Nimbus Cloak: Gain armor in addition to MS. (no MR because it would step on Nullifying Orb)
Absolute Focus: Gain armor and MR while active.
Waterwalking: Slowly gain a health shield while in the river, up to a maximum of 10% of your health.
Inspiration
Glacial Augment: Steal a flat amount of armor and magic resist from enemy champions slowed by this. The amount you can gain stacks.
and Nullifying orb shouldn't even exist