Why can't LEO's shoot? Because it's not actually a major component of their job. We pay them to do a lot of things, and shooting is only one itty bitty, teeny weeny part of that job description. More often than not, a non-LEO civilian will be better practiced with a firearm than most officers, and the FBI as an LE agency isn't immune to that fact. Equally, we don't pay them to be as fit and strong as Division 1 linebackers. When you look at the physical course requirements the shooting qualification courses, the bar isn't set very high.
These aren't elite military operators (although some where in past lives), they're a lot closer to an average Joe in terms of physical capacity and marksmanship skills.
So while my splits with a 40 S&W or my favored 357sig might not be significantly different than those with a 9mm, it's not fair to place the same expectation on Agents or Officers.
Guys around the nation carry 38spcl revolvers every day - a round which was phased out of law enforcement and FBI use generations ago. The .40 S&W isn't going anywhere for civilian use. 9x19mm was the most popular centerfire pistol cartridge in the nation by a long margin before these changes, and it will remain to hold that title now after the FBI has changed over.
Something else worth noting in these decisions - special weapons and tactics teams are more prevalent than they were when the FBI (and LE agencies) swapped from the 9mm to the 40S&W, and the equipment held for the average officer is much better than it was 20-30yrs ago as well. In the Miami shootout, often cited as a major driving event behind the abandonment of the 9mm, however, in detailing that event, you'll note the officers & agents faced semiautomatic rifles with shotguns, pistols, and revolvers. I was young, but I remember the tide change when local Sheriff Deputies and State Troopers were outfitted with carbines in the 90's.
So what I see out of it all - the 9mm was found wanting, then the 40 S&W was a stop gap before they've realized no pistol is suitable to replace a rifle. A time for every tool.