Several comments were made on inter-war Japanese faulty command structure preventing proper fire response. Also, comments were made about carrier usage doctrine flaws. Although i believe the both problems are solvable if proper historical trigger is available (for example, proposed bad incident with Hosho in 1923) i must point out what other world navies are not prevented from taking the same lessons as Japanese. Information security in inter-war Japan was pretty low, so any Japanese doctrine or construction finding would be readily copied, making not much overall difference in the flow of WWII.
What may help Japanese only is some radically insane (and dismissed as such by most other countries) but yet workable approach. The obvious improvements like better ventilation or fire training are not going to shift the balance.
Therefore, some higher-impact proposals related to Japanese carriers fire resistance:
1)Trimaran carrier with all avgas stored in outer floats. This design allows some resistance to fire and torpedo hits, plus wide, less crowded (and less prone to explosion cascade or fire spread) aircraft deck - at the expense of weight, cost and speed.
2)Decision to go with on-ship fueling trucks/railcars instead of long fuel hoses and pipes. Again, bad solution due weight, maintenance and service issues during heavy seas, but safer against fire as burning vehicles do not promote fire spread as readily as hoses.
3)Any decision to avoid carriers with dedicated hangar deck. IOTL, these affected adversely not only carriers survivability, but also an aircraft R&D due added size constraints. WWII history showed what in weather demanding hangar deck (rain or snow) aircraft utility is reduced anyway to the point of carrier being better to be withdrawn (at least before invention of radar). This point was not obvious during interwar epoch of rapidly evolving aircraft designs though, so everybody was concerned with all-weather carrier designs.
4)Anything else?