Here's the rub in my opinion, and it mainly affects the PTO setups, especially after the 1943 period when U.S. designs leapfrogged the IJN/IJA in technological superiority:
Even when we introduce the G4M and the Ki-43, the Japanese are at a disadvantage. The Ki-61, Ki-84, and N1K2 are the only aircraft in the planeset that are competitive with the mid-to-late USN aircraft. The torpedo and dive bombers perform so poorly, and are so fragile that they will never compete. Even designs like the Judy will be easy pickings for Corsairs and Hellcats. In my mind, there's simply no way around the qualitative advantage enjoyed by the US aircraft. It gets even worse when you include USAAF aircraft, especially the B-24, P-51D, etc. in the latewar period.
I desperately want to find ways to create balanced PTO setups, but from a design perspective, they are extremely difficult. We can't even have a early-war PTO setup without people remarking on how durable the F4F is compared to the A6M2's weaponry. From a historical standpoint, my personal opinion is that the IJA/IJN never had a chance in the air during WWII simply because they're designs couldn't compete, and by the time they had competitive designs, they lacked the industrial capacity to produce them.
So, my soap-boxing aside, the question at hand is how to design PTO setups that create a competitive atmosphere for both sides.