Civettone, are you implying that the B-29 cruised at it top speed with full fuel and bomb load? Ever heard of the term "cruising speed", which for B-29 was ~350 km/h, making it easier to catch for fighters.
Anyway, in my opinion the order would be like this:
J2M5, 3-speed supercharger, decent armament, but only ~50 produced
Ki-84, fastest IJAAF fighter and well armed, but unreliable because of the engine
Ki-45, well armed and probably the most durable IJAAF fighter
J2M3, 2-speed supercharger, well armed and a good climber, ~200 produced
Ki-61-II, good at high altitudes, very few made
Ki-44, best climbing IJAAF fighter, but lacking in armament
Ki-100, overrated but reliable, good dogfighter but not really the best interceptor
N1K1-J, NIK2-J, same as above and unreliable Homare engine
Ki-61-I, only barely adequate, vulnerable V12 engine
Ki-27, Ki-43 and A6M were totally unsuitable against B-29
They had more advanced types flown as prototypes, for example:
Ki-87 Ki-94-II, turbo-equipped interceptors, and a real bomber killer armament (including 30 mm cannons), top speed 700+ km/h
Ki-83, same as above but two engines
Ki-102 (even saw some service but only as a ground attacker), improved Ki-45, some turbo-equipped prototypes
A7M, Zero successor, performance comparable to Hellcat Corsair
If the above types had been in service when the B-29s first appeared, the loss rates would have been higher. But the reality is that IJAAF and IJN, while able to fight against "normal" fighters, ground attack and bomber aircraft, were not prepared equipment-wise for the B-29.