When they tried the Ki-43-IIIb with two 20mm cannon late in the war, that was the biggest problem, the increase in weight. They thought it doesn't worth the effort, and anyway there were Ki-84s and late model Ki-61 and Ki-44s available at the time which were better B-29 interceptors, if i'd change the Ki-43 i'd rather have them put it in production as soon as possible (in 1940 rather than spring 1941), with the structural issues sorted and the increased dive speed of -II to 650kph (-I was limited OTL to just 550kph), and sorting the Ho-103 MG ammo problems. OTL they daddled for a long time until they decided to put Ki-43 in production, and just two sentais had Ki-43s at the start of the war, rest had the obsolete Ki-27. In this ATL they could have all frontline sentais fighting in Burma, Malaya and Phillipines equipped with Ki-43 leaving remaining Ki-27 sentais for secondary theaters like China and home defence. Needless to say facing working, reliable and Ho-103 armed (with good ammo that doesn't explode in the barrel) Ki-43s would be quite a lot harder for the AVG.
Actually in my TL the same i would do with Ki-45, just put the damn thing in production in 1940 as is with two Ha-25 engines, don't wait another year for the Kai version, at least the Ki-45 will be a better bomber killer in 1941 and 1942 that either Ki-27 or Ki-43.
And while at it, same with Ki-44, don't diddle around, put it in full production in 1941, at least a couple of sentais would be equipped with it in early 1942.