Japan's most effective defense against high altitude raids by the B-29 was the jet stream. These high altitude winds can reach speeds of 250 MPH. The B-29s flying from the Marianas to Japan had to fly against these winds, and they caused the ground-speed of the bomber to be reduced by the velocity of the wind. My physics teacher in high school was a B-29 pilot in WWII, and the only time he would talk about his wartime service was his frequent lecture about the jet stream. It must have traumatized the crews to have an air speed of 300 miles an hour and a ground speed of 90.
The jet stream also played havoc with bombing accuracy, being a big cause of the switch to low-level night bombing.
This is the key to the B 29s career in World War II. The bomber was the most expensive weapon system of the entire war and during the conflict was rarely ever successfully used as designed. It was a uickly discovered that mysterious jet-stream prevented, not only accurate bombing, but any kind of successful bombing above 25,000 feet. This negated the whole purpose of the 29s existence. It's ability to fly high above the opposition was its technological edge and reason for existence.
General Curtis LeMay realized a couple things after the first unsuccessful raids at high altitude. Number one was there was no opposition at any altitude. The Japanese opposition in the air was nonexistent due to lack of fuel and trained pilots. Number two this meant that he could carry-on virtual mass murder on the helpless population below, which he promptly did.
He stripped the bombers of all of their defensive weaponry except for the rear guns. Then proceeded to stuff them full of incendiaries and napalm. He then proceeded to burn to death hundreds of thousands of civilians per raid by flying in at low level and dropping these heinous weapons on the helpless populations below. Almost all the raids conducted by the B 29 we're done in this manner thus negating all of the bombers technological advances which had cost billions in today's dollars, tto design, test, and produce. All in all the whole B 29 program was a colossal waste of resources, for it rarely flew during World War II using the abilities that were so expensively developed.
It's ability to fly high and fast using it's pressurized interior was rarely used and for the missions over Japan and all in all a colossal waste of money. The same holds true for all of its defense armament. As stated earlier, all of the guns except for the tail guns were discarded and the crew members who should've been manning them did not fly the mission. They were replaced by more weapons designed in hell. Weapons that caused fire storms which literally sucked the life out of all living creatures below and causing agonizing deaths for thousands of human beings.
General La May's version of hell, was so efficient at dealing death and destruction, that many of the fire bombing raids exceeded the atomic bomb in extinguishing human life and causing agonizing pain.
The B 29 was clearly not used as intended, and could easily have been replaced by B-17s and the B-24s for the extermination of Japanese civilians.
On a side note, there is no logical reason why napalm was not banned along with chemical weapons and dumb dumb bullets. It is a heinous weapon only exceeded by the atomic bomb itself.