OP, the best gun for any purpose is the one (1) that you'll practice with, with is the same as saying that you are super, super comfortable shooting, and (2) that you will have with you when you need it. This is true for hunting, targets, and self defense.
People are different. I'm a big guy but I don't like firing the .45. For reasons that no one else can understand but I really feel, I hate to shoot the .45, so I don't, so it's fairly useless to me. The .40, I like, and I shoot. Some of my 12 gauges I love, others I haven't shot in years and the only reason I haven't sold them is laziness. Everyone but the nuttiest of the gun nuts has this experience: what you like is what you like, and you shouldn't try to talk yourself out of your own preference.
If you find that a 9mm really attracts you because it's easy to shoot, high capacity, and cheap on ammo (all of which are very much true), you should embrace it. The military uses 9's for precisely those reasons. If you are not going to fire the shotgun much at the range, and won't have it in an accessible place because it looks alarming and is hard to keep out of sight, then all that power is useless to you.
Conversations about one-shot stopping power are good to have but for most practical purposes those conversations are only for snipers and hunters. In a self defense situation -- and here I'm talking from hundreds of police investigations and police after-action reports, not just personal opinion -- your aim will probably suck, you will not have the time or wits about you to reload, and what will either incapacitate or scare off the bad guy is a fusillade of shots, not your first shot. Average number of shots fired to stop or scare away the bad buy is 3, average shots fired to lethality is above 6 (!), with any handgun (those are shots fired, not hits) (I don't know the equivalent shotgun numbers). So if self defense is really what you want, you need to get a weapon AND train on the weapon to fire many times quickly. With handguns, multiple "double tap" or three-shot bursts are the most popular training methods. With shotguns, it's typically a 3-round salvo. Be honest with yourself about whether you can handle this type of shooting with a given caliber. I can't reliably do this with a .45 but I can with a .40 or 9mm, and most ranges are happy to let you train this way. I can do it with a shotgun but the ranges near me won't let me do it (rapid fire shotgunning freaks some people out), so I have to do it outdoors, which means I don't do it, which means it's a useless thing that I can't rely on. You see my theme here.
This is a long way of saying that in a practical situation, a 9mm is a solid choice, and it's by far the best choice if you'll actually practice with it more than you would practice with the other choices. I don't actually own a 9mm, so you can rest assured that I'm not saying this because I'm a booster of it; if I were to recommend one, I'd actually recommend the .40 for the same reason most police departments have moved to it (more lethality than the 9mm, more capacity and easier to carry than the .45). It's just that I have to admit that the 9mm is easier and cheaper to shoot than the .40, has cheaper ammo, holds more, has a lot more people who really say they like to shoot it, and (at least last time I checked) has more bullet options.
My do-it-yourself install thread for a TrueTrac in the rear, upgraded shafts, and a PowerTrax No-Slip in the front:
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