The FBI has many considerations when selecting a STANDARD cartridge. They've had a history of complaints from non gun "guy" agents who don't like shooting anything, they want the least recoil they have to take. Ayoob had to testify at a Federal hearing about female agents whining about service rounds for the 38 Special back in the early 80's. Those agents always exist somewhere and some of them always complain. At some point management might just see it fit to simply standardize a smaller round and tell the people who want bigger and/or more powerful to just carry their own gun that falls within parameters.
9mm Luger is cheap and easy to come by, 40 S&W isn't dying or on its way out, but its promise is long, long gone. 40 never gained the government or private use that one would like to see to make it a generally more common caliber. The more EVERYONE consumes, the cheaper and more available it gets. 9mm is logistically superior to 40 in every single way. A lot of the decisions could be from that alone. It leads to the death cycle of a cartridge, sport shooters use it less which increases price and helps to make government agencies make the decision to discontinue it, which helps send a signal to the sports shooters to use it less, which decreases popularity and decreases production, which helps government agencies make the decision to drop it..... Commonality breeds commonality in the wold of firearms, obscurity and obsolescence breeds more of the same.
The FBI dumped the 9mm Luger in the 80's because early light weight hollow points and FMJ had real issues in terminal performance. 10mm was being pushed by serous experts like Cooper and the cartridge showed great promise, perhaps grater than the 357 Magnum, in an auto loading cartridge! Interestingly enough, in the report on why they were going to 10mm from 9mm, the FBI stated the 45 ACP was completely and fully adequate, but wanted to go with the new cartridge that had room to improve, as well as more rounds per magazine. To be honest, the FBI was 100% correct in its reasoning then; save for the fact those people who don't like big booming cartridges were going to reject it and complain about it again.
Things that have changed over that period of time till the new decisions was improvements in 9mm Luger bullets, the 10mm being chucked in favor of the 40 because people just won't shoot a hot round. By the time 40 is tamed enough, 9mm Luger isn't far behind. 9mm Luger is holding its own in the market, is cheaper, has less complaints form whiners, and the 40 is going downhill market wise. The decision to go 9mm Luger wasn't that its equal or better in terminal performance, its because other factors, including saving money (a seemingly rare thing with the government).
The whole subjective statement "we can't tell the difference between bullets in those who are shot" is weasel worded, they aren't talking about effectiveness more than they can claim "the doc working the ER can't tell the difference when it pokes his finger in it when the guy arrives on a gurney". Whenever the agency makes a choice it has to defend that choice, so they made the argument to fit the decision. The 10mm decision announcement came with stuff about wounding dogs with 38 and 9mm, not hardly scientific explanations. The FBI didn't go case by case into wounds and their effects to come to their decision. They pulled convoluted statements out of somewhere to justify.
They aren't incompetent paper pushers. I always get sick of that when cartridge wars pop up, before the FBI changed over to 9mm all the 9mm Luger fanbois called the FBI the nastiest names on the earth, called them incompetent and worthless. As soon as the FBI changed to 9mm Luger again, those same people spitting on the FBI held it up to the sky and proclaimed "These are the world's greatest experts, their word is TRUTH and FACT". What a joke. Its a case of declaring people and organizations experts and authorities based on when they side with YOU. Nonsense. Look at the science and be objective, something people just don't like to do. If the FBI switched to 5.7 tommorrow, I can't imagine the insanity on the web boards. Today's experts were yesterday's clueless schmucks, and tomorrow's clueless schmucks too?
Again, the 45 ACP has always been a good choice. Science vindicated it back in the late 80's, its bullets worked adequately back then when 9mm's were still catching up. They are still top performers now. One has to be very picky what 9mm Luger rounds he chooses, 10mm and 45 ACP have great leeway and a whole host of bullets that work. 45 ACP offers good penetration on living tissue while still causing a lot of damage in shape and size. Its not a downgrade form the 9mm Luger at all, it not only stands on its own, shot for shot it is superior.