Very cool list, but as you alluded to, there’s quite a few missing :)
In no particular order, just the ones I’d like to see:
Ki-61-I Tei Kai
Ki-61-III
Ki-100-I Otsu
A6M3 Model 32 w/ 30mm wing guns
A6M3 Model 32 w/ Type 99-2s
Ki-44-II Ko
Ki-44-III
Later J2M models such as J2M3 Ko with 4x Type 99-2s
Late Ki-43-II
XT-2
That one Ki-27 with one of the 7.7s swapped out for a Ho-103, not entirely sure it was real but it’s possible (copium)
Ki-43-IV would be here if it was made, but I don’t think they ever even tried.
Also these two are the same plane:
AFAIK the one in-game is wrong and should be renamed “Ki-61-II Ko Kai” since it has the ‘split’ armament, and a new one added with the existing name (Otsu Kai) with 4x Ho-5s