I, personally, find that the shotgun is ultra L33T at killing during S1 and S2.
But by the time S3 comes along, if you are caught with your little shottie out of your base, you are quite literally, mincemeat.
So for those dangerous times, for defending, I use a Lasgun, and for leaving the base, nothing quite like a good ol' chaingun !
Overall though, I'd say I prefer the shotgun most.
I use it most of the time, and there are few things more satisfying than shotgunning a goon.