The recoil of the .40 is sharp. I find the .45 more controllable and the ammo is relatively plentiful and inexpensive. There is more than 100 years of real world ballistic data that suggests a near perfect bullet for combat. Why change for an unproven format? You can hot load 9mm to match the .40, but why? The .45 is there for you.
Go with the .45, 100 years of succesful use can't be wrong. Many military units are begging to have the 45's back, and many police departments such as mine are starting to ditch the 40's and adopting the 45's. if the 45 didn't work, it would not be the continued success and most carried weapon of all time.
I have always found the .45 to be more accurate, but YMMV. The .40 is a snappy round and hard to control during rapid fire (double taps, ect). Honestly I sold off all my .40 stuff as I just never saw any purpose for the round. If you want compact stoping power just load a 9mm with +p. If you want real stopping power from a pistol then good old .45 is hard to beat.
I used to shoot lots of 40 with my Sig, Ruger and HK. I have since stepped up to 45 for oomph. Unless it is summer and boiling hot out, my 45XD goes pretty much anywhere with me. I am a full size American though, so I can hide the pistol relatively easy though.
i have a sig 226 in a .40 and my dad has a sig 220 in a .45. they are pretty much identical weapons, and i have put a lot of rounds through both. i actually prefer to shoot the .45, i like the recoil a little more and its easier to control. i am a better shot with my gun, and i have grown accustomed to the recoil. the other thing i really like about the .40 is the capacity, having an extra 4 rounds is kinda nice. all in all its more of a preference thing, get what fits what your gonna do with it.