Which one?

If I was going after bad guys inside my house, I'd pick the 12g every time.

I prefer a handgun for anything inside a small-medium sized home. I'm assuming you have more like 1,000-2,000 sq ft... not 5,000-20,000 with lots of open spaces.

Whenever I had to clear a room in the Army, I would transition to my sidearm.

Now, I live in 500 sq feet in the middle of a city, there's barely room to handle my ARs...so my G19 is my go-to gun.

Hardware is last in the list of MINDSET, SKILLSET and TOOLSET - for a number of reasons.

Most any firearm will do for SD/HD as long as the shooter will do.

The shooter is the critical aspect - develop the shooter's mindset and skillset first and foremost. It is a copout to focus on hardware, when it is the least critical element of the situation.

And while you are at it, harden your home (add layers of security) so that there is less of a chance anyone will try to test your mindset, skillset and toolset as a shooter. That has been discussed often here, in STRATEGIES, TACTICS and TRAINING... (which is not GENERAL, HANDGUNS/REVOLVERS or SHOTGUNS - hint )

The 'which gun is best' question is not one we work on very much here in ST&T, given the nature of this forum. Some searching in this specific forum (the Search This Forum box) on topics like 'home defense' might help - there are a lot of threads here like the one at http://www.thehighroad.org/showthread.php?t=681530. Or perhaps more specific questions about what problems (beyond choice of Gun A or Gun B) you want help with...

I would not go after the bad guy(s) in my house. I have no reason be take on the aggressor role if all they want is my TV.

I would call the police and wait in the walk-in with my 12ga to see if they enter my bedroom. If they they do, I'm threatened with serious harm, and I can justifiably act in self defense.

Otherwise, they may not even know I was home.

The shotgun is a more effective weapon for quickly stopping aggressive humans.
But it is also the weapon that will most likely be well out of arm's reach when you need it most.

A handgun is the gun that you can have with you at all times...

When you're eating breakfast, lunch, or dinner at the kitchen table.
When you're watching television or surfing the web on your computer.
When you're using the bathroom.
When you're checking the mail.
When you're walking your dog.
When you're taking the trash to the curb.
When you're in the garage working on the car.
When you're sitting on the front porch watching the sun set.
When you're on the back deck grilling some steaks.
When you answer the door bell.
Etc...

The shotgun is fantastic, but most likely it will be the firearm in the safe, or in the closet, or behind the bedroom door, or under the bed....just about anywhere except close at hand when you need it.

I couldn't agree with Fred more. Assuming you have already covered and are continually covering the things he said, it seems like an obvious choice in favor of the shotgun IMO. After all - VP Biden said two blasts will scare them away, every time!

Why exactly are you forcing yourself to choose? There are plenty of ways one can carry a pistol on their body with a long gun in hand. And plenty of those can be tossed on in seconds after waking. Don't limit yourself if you don't have to.

Personally, I'd go with the fence, the automatic lighting, alarm system (or alarm company signs, which some will give you for little or nothing), a dog if not allergic and you know how to raise and train one, security windows, security door jamb, a charged cell phone near the bed, and ...

Oh, guns?

Those can be useful if you've failed to protect yourself, or if the criminal has gone to the great lengths you put him through to get to you.

In that regard, the handgun has portability as its advantage (you can't answer the door with a shotgun discretely tucked in your pocket, large pockets and Taurus Judges not withstanding), the shotgun power (but still requires marksmanship, mind you). If you already have both, you're all set.

I'd suggest searching the web for articles on cost effective ways to improve your home security, and studying (not just reading, but getting someone to explain to you the actual application of) your local laws, as well as reading up on armed home defense considerations.

But don't go asking about the guns first. Those should always come last.