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. Nothing left with which to build an icant air defense network 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.