just a couple of thoughts:

Many citizens tend to walk around their home looking for the intruder. It is much easier in that case for the perpetratorto disarm someone that is holding a shotgun. (think someone walking around with the barrel out in front of them as they reach a corner)
Also if it ever comes down to getting real close maybe even a hand to hand situation a handgun is much more effective as all you need is a little room to be able to get off a shot.

However, If we are talking about retreating to the farthest room, turning on all lights and wating for someone to enter that locked room while you are behind some cover then I'll certainly take the shotgun.