There is very little substance to the article that references real specific shortcomings with the weapons that weren't intentionally designed into the platform -- no weapon system can do everything perfectly -- and trade-offs in capability are to be expected to get the maximum performance in the general case.
Excellent observation. This also applies to most of the posts. Though well intentioned, there is a lot of mythology out there, especially about the difference between the 9mm and the .45. The energy of both is practically identical, and the only studies worthy of the name shows "stopping power" to be nearly identical as well.
Stopping power is very hard to quantify, and with full metal jacketed military rounds, you are very likely to have to shoot a determined opponent several times, no matter what military pistol caliber you use.