Both have their strong and weak points.
The .45 was adapted after the .38 fell short on knock down during the Moro war in the Philippines. It was also (with the soft lead bullet) the only pistol that worked within the tight confines of tanks because it didn't ricochet.
It was replaced by the 9mm in 1985 mostly because of its higher magazine capacity and lower recoil. But with the light weight of the 9mm bullet it lacks power just as the .38 did.
In places like the Middle East where your opponent doesn't have any kind of body armor this works. However against the Moros who made armor from bamboo the 9mm like the .38 would likely prove too weak a round, making the .45 the better choice just as it was 100 years ago.
Worthy of note is the FBI rejected the 9mm for its lack of penetration against targets such as someone behind a windshield. They often opt for the .357 Magnum for this reason.
Today's military ideology is to throw massive quantities of bullets at the enemy. In Vietnam we fired 50,000 rounds per kill. Today that number is close to 300,000. It might easily be more effective to just dump bullets out of B-52s and hope they land on targets.
Considering that the Defense Dept. is estimating a cost per troop in 2014 of $2,2 Million it might well be a lot cheaper as well.