While there is no doubt that 9mm has improved tremendously since the FBI shootout in Miami, it just defies logic to conclude, strictly in terms of terminal ballistics, that it's now the full equal to the .40 S&W. Where 9mm likely surpasses the .40 S&W is in shootability and (at least by a small measure) in capacity using flush mags.
So, it's a trade off. You just have to decide on which side of that tradeoff you fall. For an agency having to supply one handgun model/caliber to every armed agent/officer, there's a preference for a one-size-fits-all approach, i.e., the best common denominator, which seems to be the 9mm. That doesn't mean, however, that the 9mm is the best choice for you.
You might be someone who shoots the .40 as well as you shoot the 9mm. In which case, now you are down only to capacity as the factor favoring the 9mm, which might push you over the edge into the category where .40 S&W is the slightly better choice (even despite giving up a couple of rounds of capacity), due to its superior (and we don't know to what extent that's the case, but it's certainly the case to at least some extent) stopping power.
The difference for someone who shoots .40 S&W as well as he shoots 9mm is likely marginal, but it may favor the .40 S&W just slightly, all factors considered.
