Midway

Loss of the Kidou Butai

This was a disastrous loss to the IJN. They had lost four fleet carriers and a heavy cruiser for one American carrier. Unlike the Americans, they couldn't replace these ships quickly.

Loss of Airmen and Carrier personnel

Japanese casualties numbered over 3000 while the USN lost only ~300 in comparison.

While Japan lost over 100 airmen, this was not too critical as they had 2000 trained pilots at the start of the war. But they lost over 40% of their experienced carrier crew who knew how to operate carriers effectively(refueling/repairing/rearming planes, etc.). This lack of experienced crewmen would come back to haunt the IJN in the later sinkings of carriers such as Shoukaku, Hiyou and Taihou.

American Initiative

After Midway, the Japanese were forced on the defensive. While they attempted to take more territory, they now faced stiff resistance from the Americans, e.g. at Guadalcanal. The USN now had air superiority and it wouldn't be long before this turned to supremacy. If they had the carriers lost at Midway, then they would have been able to continue offensives, or at least provide needed air cover in defensive operations.

The Japanese codes had been broken.

The IJN used codebooks, unlike the German Enigma. However, the USN had already been breaking their codes since the start of the war. They were due to get new codebooks before Operation MI was to take place but this was delayed, leading to the successful interception of their transmissions. With this information, the U.S. knew where and when the Japanese would attack.

Miscommunication on the Japanese side

An 'auxiliary fleet' of repair/transport ships was detected by the delayed spotter plane, which was likely to have been the US Fleet, but due to the bad weather the spotter plane missed them. Chuuichi Nagumo decided not to engage the 'auxiliary fleet' as the last time they had attacked such a fleet it was indeed a transport fleet. Nagumo was later informed that there was a carrier spotted but it was too late.

Radar, or the lack thereof.

While the IJN was one of the most advanced navies in the world, they were behind on radar. In June 1942, most of their ships were not equipped with radar, and thus could not detect US aircraft. On returning to Japan afte Midway, many ships began to be equipped with radar but it was too late.

The US had radar and this gave the Midway garrison warning of the incoming aircraft. They could prepare somewhat for the attack unlike when the IJN carriers were attacked, which were completely surprised by the attack.

Spotting

There weren't enough spotter planes sent out to scout for the US, and there were issues with a floatplane catapult on Tone, delaying the crucial spotting of US Carriers.

The USN on the other hand, had known for many hours where the IJN carriers were due to spotting aircraft from Midway.

Complacency

Prior to Midway, Japan had been scoring victory after victory. Their actual battles were not as bad as the wargames they had simulated, and this probably contributed to the decision to execute MI as it was.

On the other hand, the Americans were on the losing end until Midway. They grabbed this oppurtunity.

Damage Control Efforts

The US were able to pull an already damaged carrier(Yorktown) into the battle and were able to keep it afloat for much longer due to good safety and Damage Control being taught to all crew.

Contrarily, the IJN Carrier crew in general were not educated in damage control - this was left to a specialised team. This was exacerbated by the haphazard refueling and rearming that was taking place during the attack.

Bad Weather

The weather to the North-East of the Kidou Butai was not great to say the least, and this helped the USN stay undetected, especially with the Japanese's lack of radar.

Shoukaku and Zuikaku were not available.

These were their most advanced carriers. Unfortunately, Shoukaku was heavily damaged in Coral Sea and Zuikaku's airwing was heavily depleted. Shoukaku's planes could have been transferred to Zuikaku giving them 5 carriers instead of 4, but as the carrier and air crew were part of the same unit in Japanese Carrier Doctrine, this was not done.

USS Yorktown

Yorktown was heavily damaged in the Battle of the Coral Sea, and the Japanese assumed that she would either be sunk or in need or substantial repair. But she was given 72 hours of emergency repairs and sent to Midway along with the other carriers, levelling the playing field. American carriers also carried more planes than their Japanese couterparts so together with the island garrison they had almost achieved parity.