I feel that the issue with Aftershock is that it has minimal incentive for building tank stats in the first place. And squishy assassins/ranged champs with CC temporarily nullify a pretty huge weakness (squishyness) without having build any survivability outright.
I do believe it's easier to curb than people think, though.
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First off, I don't think the AD/AP ratios need to be removed. They really aren't so consequential to the problem, and aren't a key element to the exploitation of the rune. However, I do believe that the % health damage should be shifted to bonus health, rather than total health. If you really want to marginalize the damage dealers using this rune, add bonus Armor and MR scaling (excluding the bonuses provided by the rune).
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The most important one: I think that the cooldown on the rune should be increased (60s?), and that the rune should receive CDR based on bonus health built (I'm thinking 10% per 200 bonus health). To a cap of 50%. This restricts the early game advantage that certain damage dealers get by limiting how frequently they have access to the rune in all stages of the game; they'll still have access to it, and it can still have uses, but they'll see far less frequent use of it, and people will have a time frame to play around it. The duration of the resistances, however, should be increased to 3s.
The idea is to make a comparable performance dynamic to other runes in other roles; sure, an Alistar will overall do more damage and have unique kill opportunities with Electrocute, but if he builds tank, he won't benefit in the same way as a dedicated damage dealer. Aftershock's strength should shine when used by those that build survivability, while still being open to some degree of creativity for other champs. I believe these changes would accomplish exactly that.