Let me start by dividing the weapons of DoomRL into categories:
Rapids: chaingun, plasmar rifle, and Beretta.
Shotguns: shotgun, combat shotgun, double shotgun, shotgun uniques
Pistols: pistol and pistol uniques
Melee: chainsaw, knife, Cleaver, LS
Each have associated master traits and trait progressions.
Rapids get MAc, elevating them into the most powerful category even though the master trait heavily restricts access to defensive traits. The trait progression means the weapon category is rather strong from the Arena onward, although suffers from ammo inefficiency. At MAc, you get incredibly high DPS for no inventory cost in ammo. The rapids get stronger as you gain levels, to the point where they shred endgame enemies. They get plasma damage for free in the upgrade to plasma rifles.
Pistols lack the strength of rapids, suffering from damage issues and clip size problems. They are generally only used for challenge runs (AoMr or just pistol runs in standard games). They only get access to plasma though uniques.
Melee weapons have two great master traits in Vampyre and Blademaster, both of which are quite viable. Until Chained Court melee is very hard to play exclusively, but after aquiring the chainsaw, Brute 2 and Berserker melee becomes very powerful, supplying either huge amounts of health (Vampyre) or incredible speed (Blademaster). Either one grants huge armor boosts through berserking. They get plasma damage for free when they upgrade to the LS (something any melee build will almost certainly do).
Shotguns, on the other hand, while dominant in the early game, quickly lose power when faced with armored enemies. Shotgun users must build for the Army of the Dead trait if they want plasma damage, instead of getting it for free through a logical weapon upgrade. As a result shotguns aren't nearly as viable for solo-weapon-type runs. There are good shotgun uniques but none with plasma damage. A shotgun build must either sacrifice plasma (losing a lot of damage in late-game) or extra traits (Army of the Dead blocks Fin, HR, and EE). Either way they have a crippling late-game tradeoff the other mainline weapon categories don't really face.
Note: by getting plasma "for free" I mean that the plasma damage is an attribute of a weapon that is already desirable due to higher damage dice. For example, LS does 8d8 over 4d6 for chainsaw, PLUS plasma.
So now it becomes an issue of game vision. If the shotgun was always intended to have a supporting role, all is well. But if it was intended to be a main weapon, capable of taking the game on its own as the rapids and melees are, then shotguns should probably get a superior master trait and an alternate source of plasma damage. My own preference is a plasma damage weapon mod and a maser trait that causes shotguns to reload in 0 time, but I welcome suggestions.