Is the WitP model that biased towards one side? Is there routine in the code that identifies an item as Japanese or Allied and gives a bonus to one side or the other? The Japanese do receive the Zero bonus but are there other unseen coded features that give the Japanese or Allies benefits? Do the allies receive a benefit in search routines to account for intelligence?
To begin at the beginning, the answer is no. WITP is equally biased for and against both sides, in two different senses:
1) Some things structurally favor both sides (supply for example). To the extent Japan benefits from supply bonus mechanics (say ships that have way too much range on way too little fuel), the same thing applies to the Allies.
2) Some specific advantages are coded in for each side. Mike Wood disclosed not long ago how the Allies are more likely to rescue a pilot than the Japanese are. Probably more of these sort of rule differences benefit the Allies, but also probably the ones that benefit the Japanese are more significant.
As for the Zero Bonus, I think it is grossly understated: "The Oscar was almost as much a technical surprise as the Zero was" Francillon. The Turning In Maneuver was adopted by the JAAF and UNTIL it was understood, the Allies were at a disadvantage EVEN WHEN they had better performance. The Zero Bonus is correctly designed in that it does not last forever - but while it lasts - and in the context of the numbers and quality of Allied planes in the forward areas - it probably matters a great deal more than, say, better rescue for Allied pilots does. So while many things, particularly logistic and efficiency and technical things, benefit the Allies, there is a time imbalance: Japanese advantages occur early and Allied advantages occur later. This seems historically accurate and nicely done IMHO.