Lack of ammo. They require you to get close to enemies that do quite a bit of damage to you. You're safer using a fusion or sniper rifle. To be viable, they need to do a lot of damage and stagger almost every enemy in the game.
Even with the buff, people still won't use them much. End game PvE enemies do too much damage. You're safer staying away from them.
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I really hope they would add more ammo to the shotguns with the patch.