Play with PDU OFF. That option is at least as valuable to the Japanese as historic torpedoes, probably an order of magnitude more effective than for the allied player. 2 nationalities means they can mainstream all production to the best planes. Allied has 13 or so nationalities, so PDU is really only helpful for the British, USN and USA air groups. Dutch, Chinese, Canadian, Australian, New Zealand, PI, CW, US Marines and Indian units all have to stick with their planned upgrades. (although, I think Michael has helped with this in the new betas.) And, the allied player can't change production, so what's the benefit to changing upgrade paths if there are no good planes in the pool?
Then, play one of the mods where they make an attempt to get production to a closer reality. If the IJ player uses half his xAK's for troop transport, then it's not reality. Those ships need to move resources, supplies, oil and fuel. Not troops. Da Babes and Treespider are working on the economic model a bit.
Finally, make training a pilot a 2 year process. After the 42 carrier battles, and the early 43 sweeps over Rabaul, Japan started training pilots. By the Philipine Sea battle in June '44, those 'new' pilots still sucked. That was about 1.5 years after they started their training program. From what I can gather from some of the AAR's (I don't do pilot training myself), it takes more like 3 months to get decent pilots out of the training program? I think IRL the US kept their pilots in training for 2 full years before they saw combat.
Of course, there's still the issue of too easy logistics for both sides. The IJN gets the benefit in 42, the Allied player gets the benefit the rest of the war. The Babes team has tried to make some good changes to slow down both sides dramatically, but I haven't played that scenario. I hope it works, because the allied player should not be invading PI in late 43/early 44, assuming a competent IJ player.
So, in summary, economics, pilot training and logistics are probably off by a small or large proportion to real life. Some of the mods have helped to correct one or more of these, but stock is probably going to stay the same.
The older I get, the better I was.