Why didn't the Japanese develop air defenses after the bombing of Tokyo?

With what? By the time Tokyo became a regular bombing target, Japan was fast running out of resources. Japan didn't prioritize air defense in their policy. Japanese battleships and carriers had less air defense and much less accurate air defense on board, compared to US vessels. The same goes for the army and Japanese air defense in general.

The Doolittle raid also played a roll: it took place during or shortly after an air raid drill. According to Japanese authorities, the drill showed resources were adequate.

Question:
Why didn't the Japanese develop air defenses after the bombing of Tokyo?

Japan was a feudalistic agrarian state throughout WWII. They were massively outmatched technologically and economically. They had trouble feeding their population and taking care of the prisoners of war they captured(*), much less fight a war of attrition on the scale which WWII ended up becoming. They made a conscious decision to hold back significant reserves for the impending invasion of Japan's home islands and this included thousands of aircraft. Simple put in 1945, they didn't have the economic resources to both commit such large resources to their reserves and significantly improve their existing air defenses. see Operation Ketsugō

(*) Bruce Johnston's "Japanese Food Management during World War II."

Here are some production numbers. Military Production during WWII

                           Tanks & SPGs     Artillery      Mortars     Machine guns
      Britain                   47,862        226,113      239,540      1,090,410
      United States            108,410        257,390      105,055      2,679,840
      Empire of Japan            4,524         13,350       29,000        380,000

Aircraft

                           Fighters    Bombers      Total Aircraft
      Britain              38,786      38,158        177,025    
      United States        99,465      96,872        295,959
      Empire of Japan      33,405      11,943         64,484

Ships

                           Aircraft       Battleships    Cruisers                     
                           Carriers
      Britain                65                20
      United States         124                23
      Empire of Japan        18                 2

@DevSolar Overall correct, and the numbers are nice, but there should be a caveat that Britain and the US did split their forces among theaters, while Japan fought only the one. (Doesn't change the fact though, Axis was outproduced right off the bat, which was part of how WWII came to be in the first place.)

That's true. The US fought the pacific war with only about 10% of it's industrial capacity. The majority of it's war materials went to fight in Europe. However in 1945 after the fire bombing of Tokyo war materials were definitely shifting to the pacific as the VE day in Europe was only two months away. Bombing of Tokyo was 9–10 March 1945 VE day was May 8, 1945. I read once that the US economy provided more than 2 tons support war materials (measurement tons per man table) for each of the 100,000 Marines who hit the beaches at IwoJima.. Contrasted by the Japanese economy which provided less than 50 lbs of support materials for each of the 20,000 Japanese defenders of that island. WWII for japan was a colossal mismatch even given it was a two front war for the US.

@LangLangC 65 carriers for The Navy? I know the angle used here, industrial capacity and planning ahead, emphasis, etc; but still. Seems you might have to qualify how many were built, just planned/started, and operational – LаngLаngС 14 mins ago

@LangLangC All of them were built. The UK had 65 operational Aircraft Carriers in 1945 see table on total strength and losses... Of coarse most of these were escort carriers and not Fleet Carriers.

If you want to talk Fleet Carriers the UK built 4 I think during the war. The United States built 36 Fleet Aircraft Carriers The Japanese did not build a single capital ship after Pearl Harbor. Not one capital ship of which construction was begun after Dec 7 1941, was deliver to the Japanese Navy during WWII.

from @MichaelB76 - Quite a few errors in your production tables I'm afraid. The total aircraft listed for Britain is less than the number of fighters and bombers.

Fixed that thank you.

from @MichaelB76 Also, the UK and US did not produce 20+ battleships, that was the total size our their fleets, mostly ships of WW1 vintage. I can't make any sense of the Naval forces table on Wikipedia, it's pretty mixed up. – MichaelB76

I just looked into the United States numbers. It appears the original source of 23 battleships is accurate broadly. With two caveats. (1) They include Battle Cruisers as Battleships, which the Washington Naval Treaty of 1922 equated with battleships calling them both "capital ships".

Washington Naval Treaty, London Naval Treaty, and Second London Naval Treaty all equate Battle Cruisers and Battleships.

Washington Naval Treaty
- A ten-year pause or "holiday" of the construction of capital ships (battleships and battlecruisers), including the immediate suspension of all building of capital ships. - Capital ships (battleships and battlecruisers) were limited to 35,000 tons standard displacement and guns of no larger than 16-inch calibre. (Articles V and VI)

(2) Second caveat and this is a big one, It doesn't distinguish between ships which were commissioned into service and ships which were ordered by congress but were never commissioned into service because production was canceled.

List of American "Battleships" who's production was awarded by congress

North Carolina Class
(1) USS North Carolina commissioned 9 April 1941
(2) USS Washington commissioned 15 May 1941
South Dakota Class
(3)USS South Dakota
(4)USS Indiana
(5)USS Massachusetts
(6)USS Alabama
Iowa Class
(7)USS Iowa
(8)USS New Jersey
(9)USS Misouri
(10)USS Wisconson
(11)USS Illinois (production cancelled) (12)USS Kentucky Laid down March 1942, launched January 20, 1950, never commissioned
Montana Class ( All were cancelled before delivery )
(13)USS Montana, (production cancelled)
(14)USS Ohio (production cancelled)
(15)USS Maine (production cancelled)
(16)USS New Hampssure (production cancelled)
(17)USS Louisiana (production cancelled)

Alaska Class (Battle Cruiser)
(18) USS Alaska Commissioned June 1944
(19) USS Guam commissioned sept 1944
(20) USS Hawaii launched 3 November 1945, never commissioned
(21) USS Philiippines
(22) USS Puerto Rico
(23) USS Samoa

Alaska Class Cruiser
USS Philippines (CB-4), Puerto Rico (CB-5), and Samoa (CB-6) were planned as the fourth, fifth, and sixth ships of the class, respectively. All three ships were to be built at Camden, New Jersey, but they were cancelled before construction could begin.

The best defense is a good offense

If we only defend, we lose the war ~ Kembai Shimata.

This answer will not duplicate the resource analysis a couple of the others did, but approaches the question based on the strategic concept of the Japanese war effort from 1939 through about 1943/44 - after which point the noose had began to tighten, US unrestricted submarine warfare was squeezing the Japanesse economically, and the end was a matter of time once (1) the US were back in the Philippines and (2) the Island hopping campaign ground to its inexorable conclusion.

0. Expand holdings in Asia for defense and resources.

Taking advantage of the European war to expand their holdings in Asia (in 1940, the Vichy French for example let them into Viet Nam) and reacting to American poloitical counter moves they sought to create a significant buffer zone around Japan.

If the Japanese, with their large, well-equipped armies that had been battle-hardened in China, could quickly launch coordinated attacks from their existing bases on certain Japanese-mandated Pacific islands, on Formosa (Taiwan), and from Japan itself, they could overwhelm the Allied forces, overrun the entire western Pacific Ocean as well as Southeast Asia, and then develop those areas’ resources to their own military-industrial advantage. If successful in their campaigns, the Japanese planned to establish a strongly fortified defensive perimeter extending from Burma in the west to the southern rim of the Dutch East Indies and northern New Guinea in the south and sweeping around to the Gilbert and Marshall islands in the southeast and east. The Japanese believed that any American and British counteroffensives against this perimeter could be repelled, after which those nations would eventually seek a negotiated peace that would allow Japan to keep her newly won empire. (Source = Britannica)

Raw natural resource considerations aside, the Japanese loss of the carriers at Midway, and the loss of a great many pilots during the Marianas Turkey Shoot, left them without the resources necessary to create a better air defense scheme similar to that adopted by the Luftwaffe from 1942 - 1945. (And they had their own resource problems). Their further setbacks in the CBI theater only exacerbated the problem.

To summarize: their initial Air Defense concept for the home Islands was to build a large enough buffer/perimiter such that Japan would be beyond reach.

1. The Doolittle raid happened while the Japanese were ascendant - before Midway

Should they have started creating an integrated air defense after the Doolittle Raid (and thus have one in place by March 1945? That would not have fit their strategic concept. (And hind sight is 20/ 20)

Before Midway, and after Pearl Harbor and the overrun of the various European/American possessios in South East Asia, Japanese strategic view remained tied to the "multiple rings of defense" mode: they kept expanding the outer ring of their bases to make it harder and harder for American planes to reach Japan. Expending precious resources on air defense rather than making it harder/nigh impossible for American aircraft to strike Japan was counter to that strategic template. It is worth noting that when the Americans showed up on Guadalcanal, those Islands defenses were still being worked on. The creation of the defensive Outer Ring was disrupted by their enemy before it was in place. You could call the Guadalcanal campaign "a spoiling attack" and not be too far off.

2. Success on Midway would render future air raids moot/too hard

The Midway operation was a logical continuation of the strike on Pearl Harbor: the long game was to convince the Americans (and others) to negotiate a ceasefire/end of hostilities by being in a position that was too much trouble to try and overcome.

On September 4, 1941, the Japanese Cabinet met to consider the war plans prepared by Imperial General Headquarters, and decided:

Our Empire, for the purpose of self-defense and self-preservation, will complete preparations for warGGranted, Yamamoto's reservations about the Empire awakening a sleeping giant eventually came true.

"We can run wild for six months or maybe a year, but after that, I have utterly no confidence."

With Midway in hand as part of that six months of "running wild" - the amphibious landings never did go off - their ability to use both land and sea based air power to keep the Americans at arms reach would be further realized. The failure of that operation not only deprived them of a land base for air operations, but also cost them significant sea based air assets.

3. The Doolittle raid was a spoiler raid/psychological operation

Back to "but they'd been bombed back in 1942" ... that raid was as much intended for domestic consumption, in the US, as it was intended to let the Japanese know "we can reach you, and we can hurt you." But if you look at the size of the raid, and compare it to raids launched in 1944 and 1945 from Island bases, it was puny. It could not be expected to do more than send a message. The Japanese, correctly from their strategic position at that time, didn't use the Tokyo raid (April 1942) as a sign that they needed to make any significant change: the buffer zone construction was still a work in progress.

4. Outer Ring was expected to last longer than it did

The Japanesse strategic estimate was correct in predicting that UK and US would take a "Europe first" strategy, but they underestimated the speed of response from the US in the Pacific in terms of mobilization and strategic counteroffensive. And they chose to expend resources in trying to not lose the outer ring, which fit their strategic concept, rather than beginning to plan for failure.

5. Little left to build a significant air defense network with by March 1945

By the time they needed to create coordinated air defense network for the homeland, it was (1) a bit too late and (2) a matter of scarce, and scarcer, resources as already mentioned in both rs29's answer and JMS' answer. There was a lack of pilots (see Kamikaze efforts previous to this), lack of planes, and an overall crippling of the economic base for waging war during the period mid 1943 to early 1945 as both the maritime theater, and the CBI theater, ate up resources in men and material for little to no gain as Allied successes built upon each other.

They might have wanted to, but they could not at that point in time.

This answer relies on a fusion of a wide variety of sources, and a detailed study of both American and Japanese strategic visions at Staff College over 20 years ago.