Ack-Ack, this is what the Japs had that was design to take on the B-29:
Ki-84 but not sure which model.
Kawasaki Ki-100 was the best AC that IJ had that showed good qualities against the B-29. Armed with 2 x 20mm and 2x 12.5 mm, great speed at high alt. but only 395 where built. It was equal the the P-51, La7 and Ki-84.
But for the most part, the Zero was the most produced AC the jap build and counter the B-29. Not sure the A6M6 had the ability to take on the B-29, A6M7 was designed for Kamikaze and A6M8 only had two prototype that could have been the most advanced AC for them.
The problem was that the Japs did not put much effort in designing better AC like Germany did. For two reasons:1) we where not bombing them around the clock like we did in ET, 2) Most of the air battle would be sea base then land. By the last year or so of the war, they had developed newer and better AC but little was done to get them into action.
Here are some AC that could have took on the B-29:
Nakajima Ki-87: had the ability to counter the B-29 with 2 x 30-mm. Only one build.
Rikugun Ki-93: was a twin eng, armed with 1× 57 mm Ho-401 cannon in ventral gondola and 2× 20 mm Ho-5 cannon in wing roots. Only 2 produced.
The Ki-94: was designed as a high alt fighter to counter the B-29, but only one was produced at the end of the war.
Kyūshū J7W: a navy base AC that, i must say, advance design for its time. armed with 4 30mm cannon, max speed of +450, but only 2 build.
Nakajima Ki-201 was the Me 262 version but none produced.
Mitsubishi J8M was the Japs version of the Me 163. They knew that the B-29 was going to be a issue so they needed something that can up fast and clime high in short time. Only 7 built none saw action.