Me and my friend had a long discussion about this recently... he's in a division of Special Ops and also swears by the shot gun for basically all of the reasons mentioned in this thread (even the "sound" of the shotgun).

However, for how my house is set up and with kids, my choice is a handgun. It's a bit hard to explain but because of how my house is setup, if someone's breaking in (and im not home) my wife (who happens to be a great shot btw) knows the drill is to get the kids in my sons room at the end of the hallway, close and lock the door and dial 911. If someone comes up to the door, announce that she had a weapon and that police are on the way (FYI we're 2 miles from the police station and 1/4 mile from a fire station). If they're dumb enough to try coming though that door..... they're done. She can hit an index card with a .45 with ease from 15' away, she's not going to miss someone coming through a door from 8' away. Reason for the pistol is I want something that my wife can handle with one hand if needed (say to keep the kids at bay and cover their eyes/ears). It's also easier for us to conceal in a small locked case.