My main reason for a rifle is simple; I have one in my hands nearly every single day, keep one in the vehicle at work and dry practice with one daily. The same can be said for the handgun, but we all know both the shotgun and rifle are far better choices.
Secondary reasons fall to my shooting style and training. I'm in the camp that whether we're defending ourselves with a rifle, shotgun or handgun, multiple hits deliver as fast and accurately as possible are a good thing and this is how I train. Even if I take the Benelli to the range, ever single drill I run involves multiple shots. For me, with a handgun or rifle, as soon as I'm on target and have elided to fire, that first round is quickly followed by a few more, then assess. The rifle obviously fits this role better for me.
Last year or the year before, we had a string of home invasions. Four men, meth addicts we later found out, were kicking in doors. At least two were armed and all were wearing soft armor. These home invasions were violent, aggressive and fast.
I have two children, they sleep on opposite ends of the house. I need to get to them in an emergency, so staying put is not an option. God forbid that a couple of guys made it into my home armed and wearing soft armor, I'll need to rapidly defeat the soft armor and devastate whatever is behind it. For me, a 10.5" 5.56 rifle loaded with 75gr TAP or Black Hills 50gr TSX fills that role nicely. Especially once I get to the kids and my daughter won't budge and I have to carry her.
It's a personal thing. The shotgun is a great choice as long as we avoid birdshot. But for me, it's not.
I think the only way to know for sure the pros and cons of each, is to spend 15 minutes a day, give or take, for the next couple weeks doing dry work at our homes. Before that, we should attend advanced training and preferrablt some shoot house classes. Until we are taught how to properly use each weapon, we really can't know what is "best", all we really know is what we're comfortable with.
I DO NOT want a big bore rifle or a bolt action for home defense.