From people I talked to it was all of the above. I know there were several issues that got traced back to after-market mags, but I have heard from various people who deployed to Iraq that they did not like or trust the M9. In my opinion the manual of arms on a Beretta is overly complex. IE the down stroke of flipping the safety on a 1911 VS the up stroke on the M9. Depending on the soldier the M9 is bulky and the DA trigger pull is long and somewhat heavy as opposed to the crisp SA pull of the 1911.
You simply cannot ignore history. The 1911 has been in all types of terrain and fought several wars. Some of the most elite units in the US, and the world, still choose a 1911 platform. Is it the end all be all? No, but that doesn't mean it still isn't one of the best fighting pistols ever made.
FWIW I've never fired either in combat, but I've put plenty of rounds down range and worked on both in a training environment. I prefer the 1911.
Also, I'll add that your desire to leave the caliber debate out of it would make me think you yourself believe that the .45acp is a superior round. I don't buy the caliber BS myself, I'm a shot placement guy, but I think telling someone to "get real" over your opinion is a little silly.