I do personally prefer the shotgun for Home Defense. Naturally as many brought up, in a struggle at close quarters its not ideal. Both handguns and shotguns have their advantages. However, some considerations can make a shotgun a more effective/shorter platform.
We have a Mossberg 500 with pistol grip and folding stock with the streamlight tactical light thats integrated with the forend. Its not "impossible" for a lady with practice/conditioning to fire any less effectively than any man. Since your wife is experienced with 12Guage she may be an ideal candidate
In manmy ways if waking up groggy the shotgun is more intuitive....find it easier in dark. Even in just pistol grip configuration we found that she can orient and remain accurately on target easier than her SP101. Of course, if carrying or pulling a young child to a safe place the handgun would be easier for reacting to an intruder.
Our round of preference is Hornaday Tap 12ga Buckshot that she can handle OK
BTW, the red box is labeled semi-auto only...the black boxed works in pumps.