First, his experience serving in WW II left him skeptical of the military brass. He was not very gung ho on war as the answer to the world's problems. He distrusted the Joint Chiefs and often tried to work around them. Of course, the Chiefs hated that about Kennedy.

Also, and this was especially true after the Bay of Pigs, JFK did not trust the CIA. He kind of thought many in the intelligence service were crazy. Another group he tried to work around.

And, I think JFK was much more hawkish when he first took over than he was even 6-12 months later. Having his finger that close to the nuclear button changed his views. I'm not saying he became a pacifist, but it does seem he was sincerely looking for other ways to fight the Cold War, ways that de-escalated the chance of war with the Soviets.

He was surrounded by military men who saw everything through the lens of war, and who were still flying high off the win of WW II, and who thought we should make use of our nuclear weapons.

With some, added power leads to added ego and irresponsibility, though since we didn't go to nuke war, one assumes LeMay at least wasn't insane or completely irresponsible -- just a lot more willing than most to want to go to war with the Commies.  And JFK got so frustrated listening to his warrior rantings one day that he left the meeting early, and angrily told an aide never to allow LeMay near him again.  

He simply had less megatonnage in WWII and smaller, more difficult and smaller delivery systems. I'll have to review his ETO time, but a couple of points on his time fighting Japan: LeMay pushed for firebombing population centers at night. in the 1940s, most housing in japan was still wooden and paper.

LeMay, in my opinion, wanted to destroy the Japanese population, not simply the infrastructure.

But I can't single LeMay out. With the exception of MacArthur and his Southwest Pacific staff, the attitude toward Japan and Japanese was ethnocentric to the point of, if not proposing extermination, then not being concerned if extermination was a by-product. However, Navy leadership, with the implicit approval of Washington, accepted this.

In part because of the ferocity and complete ideological submission to the war effort of the individual Japanese war fighter.

I'd still say that LeMay was on the borderline between genius and insane genocidist. He probably went back and forth across the line.

But to come to his defense, or at least present a different side, LeMay and his staff accepted, quickly, that even with the B-29, high altitude high explosive bombing was ineffective.

First, the jet stream was not known as a meteorological effect, slowing down high altitude bombers to the same speed as Japanese interceptors. The B-29 was supposed to be and was, usually, faster and could fly higher than Japanese interceptors. With the jet stream winds, the bombers were slowed tremendously, and fuel issues combined with effective air interception led to unacceptible losses.

To combat this, LeMay ordered night time bombing. Just like British nighttime bombing, the targets had to be strategic, such as population centers in general, instead of the precision bombing seen by US daytime bombing in Europe.

LeMay swiched from high altitude daytime  high explosive bombing to low-level incendiary non-precision bombing. He even ordered the removal of defensive armaments, such as machine guns, from B-29s. No need, given nighttime and low-level, in his evaluation.

A hyndred thousand civilian deaths in a firestorm in one of the raids on Tokyo in one night... like Dresden and the British.

More to say, but at a later time.

Personally, I think LeMay was insane, but in a manner considered useful. After the war, rank and seniority, and some way of keeping other high ranking generals from challenging him... the splitting of the Army Air Forces from the Army, creating the USAF...

The person with the best results during WWII but still young enough, educated enough, with enough engineering expertise and strategic vision in a new, atomic era, seemed to be LeMay.

And Kennedy did act, when and where he could, to replace some of them -- Dulles and a few of his lying subordinates at CIA (over the BoP deception), CJCS Lemnitzer, ultrahawk ass't nat'l security adviser Walt Rostow (sent out of the WH and over to State, out of Kennedy's hair, now a non-factor; LBJ would later bring him back and name him as nat'l security adviser).  Insubordinate and reckless Navy Chief Geo Anderson essentially fired after the Missile Crisis.

But it wasn't a question, with the military in the Cold War, of replacing a Lemnitzer with some dovish general, not that there would have been many around back then.  JFK wanted intelligent and loyal people but not a bunch of Yes men, and politically he was in no position to replace them all with antiwar activists and conscientious objectors like his aide Sorensen.  

So ultrahawk wildman Lemnitzer was replaced by a mere garden variety hawk, the sharp and reliable Taylor, which was a vast improvement and a switch that worked out for Kennedy.  And Max Taylor was about as "liberal" a general (though he was not, just not hawkishly insane) as the Pentagon political "market" would allow back then, imo -- any more left, and JFK would have had a military mutiny on his hands, Seven Days in May variety.

Allan Dulles at CIA was ousted, but Kennedy though of a mind to "splinter the CIA into a 1000 pieces and scatter it to the winds" (as he said post-BoP) wasn't quite ready to do this with a real flame-throwing reformer type, so opted for a bipartisan moderate Repub replacement there, and the results were mixed though McCone, unlike Dulles, probably was loyal.  And more comprehensive reform of CIA was put off to his 2d term when one of JFK's thoughts (as Bobby noted later) was to name RFK to head the agency.