So minor point of order first, Midway saw the loss of just 4 IJN carriers (Akagi, Kaga, Hiryu, Soryu) with the Zuikaku and Shokaku left behind in Japan still licking wounds from the Coral Sea.

But the larger point is built on several faulty premises.

1. That all carriers are created equal.

2. What IJN strategy and operational thinking looked like post Midway

3. The operational realities of IJN Naval Aviation by 1944.

To the first, carriers are not interchangeable. The Japanese Navy had about 12 hulls that fit the definition of aircraft carrier by the middle of 1942, so post Midway that still leaves them with 8 or so.

The problem is that many are older, slower, or conversions from merchant or auxiliary ships, which mean additional compromises in designs. Everything from having a painfully small airgroup, to being barely fast enough to operate with front-line task forces, to having hangars and elevators not large enough to operate the most modern designs. This meant that for the time being the IJN was left with just Shokaku and Zuikaku as its entire force of truly modern and effective fleet carriers, often paired with 1 or more of the lesser vessels like Ryujo(a 1930's vintage design relegated to light carrier status) or Junyo( a converted passenger liner).

Both sisters would be committed to the fighting around Guadalcanal in the Fall of 1942, indeed for all the press the Coral Sea and Midway get, they were just 2 of the 4 great carrier battles of 1942. Eastern Solomons in August and Santa Cruz in October were just as impactful. Pitting roughly on par IJN and USN forces against each other, which while the USN came away bloodied and missing key carriers, the IJN was never able to gain dominance in the waters around Guadalcanal or choke off USN efforts to keep the island supplied.

This gets into the 2nd point. The escalating conflict in the Solomons and later US landings in the central Pacific, combined with a depleted carrier force meant many IJN naval aviators found themselves sent ashore. The fighting in the Solomons would do much more damage than Midway to the trained body of men that made up the prewar Japanese naval aviator corps. And replacements were not an overnight process and required not just flying time, but time to become proficient in the dangerous task of actually operating from a carrier. Thus 1943 actually becomes something of a quiet time for IJN carrier ops, with ships being repaired, a few plans cancelled before they went off, and a general reorganizing.

Larger, newer, and better designs were of course something IJN leadership understood it would always need and all through the war Japans overwhelmed shipbuilding industry attempted to meet the demand. And by 1944 they had at least produced a few new hulls. Namely the new fleet carrier Taiho, and was working on the Unryu class(essentially updated Hiryu hulls) and was able to get the existing fleet back in action.

But this hodgepodge force of 3 fleet carriers and 6 light carriers was not of anything like the same quality as the Kido Butai of 2 years before. Especially when it came to aircrews. The carrier force had been forced to retreat to anchorages in Sumatra and training time was very limited, and even acquiring enough fuel was an issue. This compounded the qualitative advantages the USN Fast Carrier force was already bringing to bear in any engagement.

But in some ways this was setting the stage for what had always been the idealized way for the IJN to win a Pacific War. Grind down the enemy until they reached the Philippine Sea defensive islands, wait until they were pinned in place or caught in a vulnerable position, utilize a combined arms approach with naval aviation, shore-based air, and light forces like subs, with heavy surface forces on hand for final blows. So if you squint and ignore all the major issues, like having to exchange bunker oil for crude oil straight from the ground to get some ships going, the stage is set. This was lining up with the IJN's 40 years of cultural obsession with a single great decisive battle to win the war despite numerical inferiority in the long run.

It of course turned into another bloodbath and the final breaking of the IJN's naval aviation capabilities in a meaningful way. Not 100% sure what you mean by Midway II, but both the original Midway Commanders Intent and A-Go 2 years later were built around the same idea, to achieved a decisive victory through a joint effort on the ground of the IJN's choosing where the USN could not or would not retreat. So by the time the US lands on the Philippines that October surface forces and land-based aviation are in essence all the IJN has left to use, along with the first deployment of the newly organized special attack units which would come to be known as the Kamikaze, the final desperate attempt to see some military use out of naval aviation which could no longer support an effective conventional force for any real offensive action.

With your comment about Halsey's actions, I also think you might be mixing up the Philippine Sea and Leyte Gulf? The Philippine Sea in June of 1944 was fought under Spruance's command on the US side.

So by the time Shinano is ready several months later its a moot point. The ship has no real experienced crew to draw on, and certainly, no great pool of experienced naval aviators to fly from her. And increasingly no smaller vessels to escort her or fuel to train or operate far from port. Leading to her being sunk before being of any real use to anyone on the journey from her shipyard to the large naval base at Kure.

If you are interested in a readable and approachable overview of the Pacific War I cannot recommend Ian W. Tolls trilogy enough:

Pacific Crucible, Conquering Storm, and Twilight of the Gods are very much the best intro I have found. I am happy to suggest additional sources for more specific topics if you want!