I don't understand all the negativity with the .40. I think if I was limited to FMJ's I would definitely want my pistol to be a .40. With the large flat nose, .400" diameter and relatively high velocity, I would feel well armed.
If I were limited to FMJs I'd pick the .45 ACP over the 9mm and .40 S&W. Luckily, I'm not limited to FMJs.
With modern hollow points 9mm, .40, and .45 are all essentially the same when it comes to actual effectiveness on a two-legged target. So I say just go with the one you shoot the best. For me, that's usually the 9mm (but not always).