Just remove the ability to melee after shooting and have a cool-down to melee again. Then, the only way to insta-kill combo is melee then shotgun(meaning you'd have to get really close to do it) or actually utilize the shotgun's rate of fire. I don't use shotguns much, but I've died by shotguns plenty to know what the problem is. This is just my opinion on how shotguns can finally be appreciated and less annoying.
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I doubt they have the skill to just code that for shotguns.