Well, if the Combat Shotgun isn't supposed to be viable in the later levels, then you need some rebalancing, because the Combat Shotgun kicks serious ass! :D I was able to kill Praetorians with six or seven shells, and that's with basic light weapons skill. (Of course, that's at point-blank range, which meant I was frequently impaled while I was shooting them, but having Power Armour and expert medical skill (later Master) made it doable) :) EDIT: Oh, and I hit the Queen with two Incendiary grenades and a Krak grenade and finished her off with Shotgun fire.
For most of the game, though, I was using a combination of whatever pistol I had at the time and a primary weapon that fires 5.56mm bullets. (I can't remember the name of the weapon, but it held 30 bullets and fired six rounds per volley) I found a sniper rifle at one point, which appeared to be more ammo efficient, but didn't kill enemies fast enough. I preferred to use the above-mentioned rapid-fire weapon when I wanted things dead fast, (like Stalkers and Elites) and switched to the pistol when I wanted more ammo efficiency. (for killing smaller or individual enemies) Using the pistol so much meant that I tended to take a fair bit of damage, but expert medical skill took the edge off of that. (I might as well play to the character's strength) ;)
So, it required a different play-style from my earlier HW Specialist game, but still perfectly viable. :)