Couple of observations:
1. You compare the performance of the fighters but do you also need to look at numbers available? In Malaya, the IJAAF had the luxury of assigning Ki-27s for base defence and using the Ki-43s for "offensive counter-air" operations whereas the Buffalos had to do everything - defend their bases while also trying to escort bombers, strafe ground troops, protect convoys, carry out tactical reconnaissance etc etc.
2. The fundamental problem facing the Allies is the perennial challenge of how and where to defend. The Japanese had the advantage of being able to mass force for their planned offensive actions whereas the Allies had to try and defend a much larger area and hence couldn't mass forces to meet the threat. Lack of adequate early warning in Malaya is critical in this regard for the air campaign (and follows on from #1 above).
3. The Japanese had their internal political challenges but it was still a single country looking out for its own interests. ABDA was 4 countries trying to work together when, up until the Japanese attack, not all had been willing to commit. Hardly a good environment upon which to develop cohesive defensive strategies or tactics.
4. For the Japanese, taking the Dutch East Indies was the "main event" whereas for the British and Americans it was really a sideshow...and force allocations (and competencies) reflected those realities.