doing 3 gun, and seeing how slow the shotgun loading goes (especially for me) I just can't see a situation where i'd pick a shotty over an AR.
I guess if you knew you were only going to be shooting whatever your mag capacity is (3 - 10 rounds), then it wouldn't be an issues, but who knows that.
Both XM-193 and 00 Buck penetrated at least four walls.
As for my personal preference, I currently have a Mossberg 535 on my side of the bed and a Remington 870 on my wife's side. But when I get back from my deployment, I'll finish building my AR and it will take the place of the 535. If you could guarantee me that I'll never face more than one intruder at a time, I would go with a shotgun. But if I need to make shots on multiple targets, I would rather have an AR. Plus, the option for up to 29 follow-up shots.
Get both. Different uses for both. Though their uses do overlap some, one cannot replace the other. Shotgun for urban uses within 50yds, ar-15 up to 500 yds. Its hard to be specific on the uses of each one, but each one is unmatched in its own niche.
You can't beat what you are MOST comfortable with. I would say get the AR now since you won't be able to later and a shotgun when you can after that. just my $.02.