I personally don't prefer a shotgun for home defense primarily because its size, maneuverability, and convenience are not favorable in my little house. Given my situation, I prefer handguns. If I wanted to arm a safe room with a long gun for home defense, I think I'd prefer a .223 rifle for faster follow ups and more capacity.
A shotgun's biggest strength IMO is that it provides more bang per buck (quite literally) than any other option. If stopping power and cost are the biggest factors in your home defense equation, a shotgun is a good option.