In my opinion every round has pros and cons. If there was a superior, end all performer, we wouldn't have several calibers. 9mm has a lot of fan boys, and for good reason, it's cheap, lower recoil, slightly higher capacity. 40S&W penetrates better, has a bigger hole, slightly less capacity, more recoil.
To any fanboy that says one is better then the other, is an ignorant fan boy. Both have pros and cons. I think the reason some LE agencies go with the 9mm is cost savings (or recoil factor). The order of importance is shot placement, penetration, expansion. If you cant shoot 40 accurately, but you shoot 9mm more accurately, then 9mm might be better for you. If you shoot both the same then maybe you should consider 40. Neither is a magical round, all the BS in these arguments sometimes defies physics.
Over penetration is BS. Self defense loadings are meant to penetrate and expand correctly, if you shoot ball ammo then go with a 45 auto.
The 9mm does not equal the 40. Anyone can manipulate statistics to meet their goals. Ballistic jello, one shot stops, all that other BS really comes down to what you are comfortable with and what performs adequately. I carry a 380 more often then I would like because it is better than nothing and the convenience. I would prefer to carry 357 mag 158 JHP or 40 SW 155 JHP, thats me. Others prefer 9mm, which is superior to 380 in my opinion. Again pros and cons, personal preference.