I know this subject has been done to death, but I think there's more to it than what's generally covered in most discussions. I gave it a lot of thought and concluded that the shotgun is best (for me, anyway). Here are my reasons:
Price--At least half of what an AR rifle costs.
Ammo--easier to find ammo locally at reasonable cost. Again, my own situation.
Breaking in period--I've noticed that a shotgun doesn't require nearly as much to determine whether or not it will function reliably, mostly because a pump is operated by the user. If a shell sticks slightly, the user just pulls back the slide a little harder for the next shot. If a shot is slightly underpowered, it won't affect the cycling to chamber the next round. An auto like the AR depends on the ammo to work consistently for the gun to work reliably. Therefore, a shotgun could be bought, and then determined reliable in relatively few shots. For an AR, people usually recommend about 200 rounds. That can be expensive and time consuming, unless you have the money and love shooting that much.
Quick into action--When a bump in the night occurs, you want to grab your gun quickly and have it ready to shoot. With a shotgun, I find it easier and more natural because I simply have to pick it up and assume a natural hold; right hand on grip, left hand on forearm. If a threat is determined to truly exist in the house, all I have to do is pump the forearm to chamber a round. But with the AR, either the left or right hand has to come off the gun to rack the charging handle, and then reassume a firing grip. With stock features, it is easier to rack the charging handle with the right hand--which is also the one used to pull the trigger. With the shotgun, the firing grip is maintained throughout the process. Of course, this can be negated by simply keeping a loaded chamber on the AR, but most people advise against that.
Muzzle blast--Much louder with the AR. Yeah, people say your hearing is the last thing you'll be concerned about, at least until afterwards. But with the AR's capacity of 30 rounds, can you imagine taking the muzzle blast of an AR 30 times?
Stopping Power--At the close ranges encountered in a home defense situation, the shotgun will put out around 1800 ft. lbs. of energy vs. 1150 for an AR. Using that energy over the area covered by 9 pellets of buckshot would do more damage.
Post shooting aftermath--The police will come, and the DA will determine whether or not you were justified in the shooting. They will then see what you used in the shooting. Would you rather them see that you used a commonly owned shotgun, which most of the public sees and recognizes, or would you rather it be an AR rifle, which has been portrayed to the public as "evil"? Some police and DAs will latch on to the idea that you could be seen as the bad guy simply by painting you as a person who is a gun nut just waiting for someone to break in so you could spray 'em down with your AR rifle. I know it's ridiculous, but keep in mind that the general public can be quite gullible and their emotions can be swayed, and also that lawyers and the media are quite skilled in that regard.
Now, with all this said, I'd like to point out that I own both. I also realize that the AR has features that put it above the shotgun, but I don't think enough of them apply to real-world home defense to warrant giving up the shotgun's advantages. If you want something that can shoot long range, then the AR is best, but that's not real-world home defense. Rapid follow-up shots are nice too, so the nod goes to the AR for that. Capacity is also on the side of the AR, but more than 8 would be hard to imagine needing, especially if we're talking about 8 rounds of buckshot.
Price--At least half of what an AR rifle costs.
Ammo--easier to find ammo locally at reasonable cost. Again, my own situation.
Breaking in period--I've noticed that a shotgun doesn't require nearly as much to determine whether or not it will function reliably, mostly because a pump is operated by the user. If a shell sticks slightly, the user just pulls back the slide a little harder for the next shot. If a shot is slightly underpowered, it won't affect the cycling to chamber the next round. An auto like the AR depends on the ammo to work consistently for the gun to work reliably. Therefore, a shotgun could be bought, and then determined reliable in relatively few shots. For an AR, people usually recommend about 200 rounds. That can be expensive and time consuming, unless you have the money and love shooting that much.
Quick into action--When a bump in the night occurs, you want to grab your gun quickly and have it ready to shoot. With a shotgun, I find it easier and more natural because I simply have to pick it up and assume a natural hold; right hand on grip, left hand on forearm. If a threat is determined to truly exist in the house, all I have to do is pump the forearm to chamber a round. But with the AR, either the left or right hand has to come off the gun to rack the charging handle, and then reassume a firing grip. With stock features, it is easier to rack the charging handle with the right hand--which is also the one used to pull the trigger. With the shotgun, the firing grip is maintained throughout the process. Of course, this can be negated by simply keeping a loaded chamber on the AR, but most people advise against that.
Muzzle blast--Much louder with the AR. Yeah, people say your hearing is the last thing you'll be concerned about, at least until afterwards. But with the AR's capacity of 30 rounds, can you imagine taking the muzzle blast of an AR 30 times?
Stopping Power--At the close ranges encountered in a home defense situation, the shotgun will put out around 1800 ft. lbs. of energy vs. 1150 for an AR. Using that energy over the area covered by 9 pellets of buckshot would do more damage.
Post shooting aftermath--The police will come, and the DA will determine whether or not you were justified in the shooting. They will then see what you used in the shooting. Would you rather them see that you used a commonly owned shotgun, which most of the public sees and recognizes, or would you rather it be an AR rifle, which has been portrayed to the public as "evil"? Some police and DAs will latch on to the idea that you could be seen as the bad guy simply by painting you as a person who is a gun nut just waiting for someone to break in so you could spray 'em down with your AR rifle. I know it's ridiculous, but keep in mind that the general public can be quite gullible and their emotions can be swayed, and also that lawyers and the media are quite skilled in that regard.
Now, with all this said, I'd like to point out that I own both. I also realize that the AR has features that put it above the shotgun, but I don't think enough of them apply to real-world home defense to warrant giving up the shotgun's advantages. If you want something that can shoot long range, then the AR is best, but that's not real-world home defense. Rapid follow-up shots are nice too, so the nod goes to the AR for that. Capacity is also on the side of the AR, but more than 8 would be hard to imagine needing, especially if we're talking about 8 rounds of buckshot.
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(ARs are also much easier to suppress, so there's that). 
