I am not a pro with ballistics, but here are my opinions.
9mm in a light gun can be very unenjoyable to shoot. Hotter 9mm rounds have a more violent (snappy) kick than a 45. My SA XD9 kicks alot worse than my SA 1911 TRP 45. The 45 feels like a big push, instead of a violent snap. The ability to carry more rounds in a 9mm means nothing to me. 8 rounds of 45 should be enough to end most engagements. The reason a traditional 45 only holds 8 rounds is because the single stack makes for a slim comfortable grip.
The main problem witht the 5.56 is not the reduction in speed, it is the lack of mass. The lower speeds hurt it more, but a 5.56 can never compete with a 7.62, no matter what velocity. 5.56 is my current battlerifle cartridge due to accuracy and convenience, but I know it is a poor man stopper and terrible glass breecher.
357 is an incredible people stopper because it has both, mass and velocity. but is a poor semi-auto pistol cartridge due to the ergonomics that would result from a gun that could feed the cartridge. And the recoil is a problem.
45 works better not just because of a larger diameter, but also due to the mass of the bullet. a 230 grain 45 is double a typical 115 grain 9mm.
Proven results in the battlefield show the 5.56 and the 9mm to be poor man stoppers compared to what we had prior to Vietnam. All of the military will be moving to a larger rifle cartridge (maybe 6.82), and BACK TO THE 45 ACP.
Unless you really like a 1911 (superior in many aspects), get a Taurus 24/7 OSS in 45 ACP, or a SA XD 45 and don't look back.
http://www.taurustactical.com/dsp_247oss.cfm
http://www.springfield-armory.com/xd.php?model=3