There is a reason WW2 military picked the .45 for both thier standard issue sidearm(colt 45) and submachinegun (Thompson)....lethality!!
If someone were breaking into my home, and I only had one bullet for my 9mm and one for my .45 ( ridiculous analogy I know, but I'm trying to make a point) I would grab the .45 without even a second thought.
I think you would too.
The thing is, regardless of statistics, if you don't hit you don't kill, so the best choice should always be "whichever gun I am best at using, or is best for the situation" A heavier pistol can be harder to aim than a light one. If you're talking about multiple shots, you could most likely get more hits with a 9mm than with a .45 simply due to the recoil making you shoot slower, or less accurately.
On the battlefield, the sniper rifle is the hardest hitting, longest range infantry weapon. So why aren't armies issued with nothing but sniper rifles? Clearly because weaker weapons employed properly will defeat more powerful weapons employed improperly.
Real guns are far more accurate and powerful than most games admit - all in the name of balance. So the truth is, at the ranges most engagements happen in-game, anything should kill and be accurate. If they weren't then they wouldn't even be issued. At game-ranges, the only choice is "long weapon or short weapon" and that decision should be made based on the situation, not which does more damage when you hit. In fact most modern armies don't even issue pistols or sub machine guns to their soldiers because they are no more useful than a modern light weight assault rifle.
In the real world I'm not that good a shot, yet I could hit a running man sized target at 300m with ease using the NZ Army Steyr AUG. Now here is something that should make it clear what I mean: the Steyr Aug is lighter, and shorter than the PPSh, which means in any kind of engagement, the Steyr is easier to use, and harder hitting than said PPSh. In fact it is only 1 kg heavier and 5 inches longer than the standard H&K MP5!
Basically, the small weapons like the SMG and pistol are going the way of the dodo - at least in terms of standard army issue weapons - and there is a very good reason for it. Even in WW2 this was recognised and lead to the development of the assault rifle.
You need more stopping power over longer ranges in combat than the pistol or SMG can provide. Thus in WW2 you had mixed platoons with some spray and pray weapons, and some hard hitting accurate long range weapons. Modern armies have cut that down to a LMG and assault rifles, all firing the same round. The LMG is more accurate and harder hitting with the same bullet, due to being fitted with a heavier and longer barrel (heavy barrel increases accuracy, longer increases velocity), but it is also larger and heavier than the assault rifle, can tend to waste ammunition, and is more complicated and thus more likely to fail. If that wasn't the case you'd see everyone carrying M-249's rather than M-16's.
The M-249 in fact is pretty close to that "perfect weapon". In the old days you would never clear a house with an MG, because the MG was too heavy and awkward to quickly clear rooms. In Iraq, the M-249 has become the go-to weapon for house clearing because it is light enough and small enough to quickly engage targets, but it also has plenty of ammo and power.
So, to come back to what I was saying, the weapon you choose should always be the weapon that fits the situation and the user. In just about any real war situation, the difference between a 45 and a 9mm will be ammunition capacity. The 45 can't hold as much and as such is less useful, period. If a 9mm has twice as much ammo, but stopping power that is sufficient (and it is) then why carry a 45 with less ammo? You may get a slightly higher one-shot-stop ratio, but you've got twice as much ammo, a lighter gun with lower recoil and are probably not even going to notice the difference. Who in their right mind relies on statistics? No, you would put three into him whether you used a 45 or a 9mm, in which case the gun with more ammo is better.
The 7.62 is harder hitting than the 5.56, but you can carry a lot more 5.56. The M-60 used a 100 round 7.62mm belt. The M-249 uses a 200 round 5.56mm belt. Which one is issued to more soldiers now? The M-60 is longer range and harder hitting, but it's actually unnecessarily long ranged and hard hitting. The M-249 does the job better, simply by reducing the power to what is actually needed, then carrying more ammo.