I don't typically use the shotgun for my soldier shep either, but with my new game+, having a full load isn't giving any weapon penalty so I've figured I might as well use it.
For the record, for a no penalty load, I've gone with the X versions of in single player:-
Particle Rifle (Great for harvesters so far)
Pistol - Eagle
Shotgun - Disciple
SMG - Hurricane (with lightweight materials)
Sniper - Valiant
To be honest, it's not the perfect load for maximum damage, but it's doing the job so far.
During my first playthrough, it was primarily the Mattock, Eagle and incisor.