For self defense with shotgun I would definitely choose the 12 gauge simply because it is bigger and more powerful. BUT for sporting use at skeet, clays, and game birds I will continue to prefer and use the 20 gauge as I have for many years. My choice of shotguns is a Grade VI Citori O/U in the Lightning model with interchangeable Briley choke tubes. I just don't need the extra weight and power of the 12 gauge and the 20 handles quicker for me.
I think the home defense market moves a lot of 12ga, and maybe that there are more options in ammo, and accessories for the gadget guys.
I thought about buying one for HD so that my wife wouldn't be so intimidated by the shotguns recoil. We ended up shooting one, and I think because it was lighter in weight, the recoil was a more apparent that my old 12ga.
I ended up buying a Mossberg 12ga and added a Knox Spec-Ops and it made a world of difference for her. That thing makes #8 shot feel like a .223. She was even able to handle 3" mag 00 buckshot.
One of the nicest shooting shoguns I ever owned was a 16 gauge Winchester Model 12 with a 26" skeet barrel and Simmons rib. It was great the first day of dove season. Of course, back then, Winchester scaled the receivers so that the 16 was slightly smaller than the 12 gauge version and the 20 gauge was scaled down accordingly, etc. That made them very handy and quick pointing. Just look at the size of the receiver on a Model 42 Winchester, which is basically a Model 12, but in .410 bore. It is even smaller still than the 16 or 20 gauge version.
In short, what killed the 16 gauge was when the mfg decided to use their 12 gauge receivers for the 16 and when the 20 gauge mag came out. The added weight of the new guns, plus the 20 gauge's shot advantage took a toll on the 16.
I still own my first shotgun, which is a AYA Matador in 16 gauge with 28" barrels bored mod and full. It does a credible job on dove and is still a pleasure to shoot. I am tempted to buy a new Remington 870 in 16, but I have two 12 gauges which I shoot more often.