Very interesting!!
Perhaps Paradox could add a modifier for Japan to simulate what happened in real life:
•Samurai Spirit: +10% unit morale, -10% organization
Other than that, however, the lack of mobilization and production is in the player's hands.
However, I feel that this should also be said: the Japanese weren't stupid. They understood that the production of tanks and ships was essential to their war machine, but they also knew that it would be equally fatal to overproduce these vehicles and then not have enough oil to power them.
July 26, 1941, the US cut off all oil sales to Japan. The effects were immediately felt, and this is part of what drove the Japanese to Pearl Harbor and attacking the western allies. The Japanese captured Dutch Indonesia, and took advantage of its oil-rich provinces... However it still was not enough.
The Axis had the unlucky dealt hand of being short on oil the entire war. Japan certainly could've done with more tank divisions, but their technology for this was outdated and impractical anyways.
Japan made do with what it had: the awful predicament of being stuck a decade into a stagnant war, low on resources, and outmatched technology. They held up remarkably well, and it holds true to their mentality that they kept fighting after their allies had all been beaten to a pulp. Could Japan have done better? Possibly. But don't doubt for a second that with the situation given to them, they did damn well.