He nailed it at the end... shoot what you shoot best, carry what you shoot best and get the gun that fits YOU. 9mm is a good round. Low penitration when considering barrier objects such as car doors, walls, etc... good and bad depending on your outlook.
Will the 9mm kill, wound or flat out drop your target... uh yeah. Will 45 be more effective when placed side by side with the 9mm... yeah. But then again a 82mm mortor will kill a bunch of stuff in its impact area, much like it's big brother then 155mm arty shell.
We've all heard or read the stories of LEO or Mil guys having to dump 16+ rounds into a target to drop it when using 9mm... I personally don't recall those same type stories or rumor with the 45. Guess that is part of the hype, but the fact of the matter is that the 45 will stop someone more often than not even without a X ring shot. 9mm is more likely to require a few more rounds when outside the primary kill zones.
There is a whole lot to be said for 9's in general. Most of us who are both 9 and 45 fans are also huge fans of the 40 cal round, which I think has been neglected as a general use round.
Then again I subscribe to the theory that if your can't stop it in 16 rounds, you shouldn't be messing with it... don't see many 16 round .45's now do ya?