Leo,
Mostly tuning. The Ha-40 and 140 were lighter than their German cousins which had tight tolerances and these lighter versions had even more precise tolerances still. So factory worker skill was at a premium.
Another thing is the quality of the fuel in the field.
Also there is the experience of the Japanese mechanics on inline motors vs German experience.
If tuning wasn't right, it could suddenly lose power.

The ki.100 was a nasty suprise to the us. It was an awsome plane in its own right but the King and Queen of the Pacific were the F4U-4 and P-38L. Go check out there real limitations that I have discussed on this sight.

In mock dogfights between equally skilled Japanese pilots pitting the Ki 100 Goshikisen against the Ki 84 Hayate, the Ki 100 always won. Every time! Hard to see how unless you witnessed it. The Ki 84 had the level speed advantage but it was over 40 mph slower in dive speed. Granted, the Hayate could outperform the latest U.S. fighters at medium altitudes and even out-turn the Spitfire. But the radial Tony was no Spitfire. It was somehow a superior adversary (except way up high). Add to that the fact that it had a tougher hide to absorb combat damage and was more reliably powered than the Nakajima uber fighter, perhaps the Kawasaki pilot's enthusiasm can be better appreciated. Inline Tonys have been said to out-roll (at least to the left) the U.S. Navy fighters, so maybe the radial improves roll, it should (ala Fw 190A radial vs Fw 190D inline). The right turn in the earlier Ki 61 Tony was much inferior to the left turn, maybe the Ki 100's radial helped with this flaw too. What's left? All we know for sure is the weight of the vulnerable liquid cooling required for the inline engine wasn't missed. Now it was lighter on it's feet.

If it came out of a high speed dive it was fast. The Kawasakis were the only Japanese fighters that could hope to dive with the Mustangs. Otherwise it's true that level speed was inferior to it's fore-bear, the Ki 61-II Tony (if it was well tuned). But the Ki 100 Tony dropped the weight of the liquid cooling on the inline engine, improving it's handling. The less vulnerable radial was more reliable than other late model Japanese radial fighters like the Jack, George, and Frank. Also much sturdier than the Tojo or slower late model Oscar and Zero. At a time when Japan's young fliers had abbreviated training, such a more simple 'pilot's plane' was made to order. It proved itself a success against U.S. raiders (especially the Hellcat) out of all proportion to it's numbers at the end of the war. Maybe best isn't the word. Surprisingly effective might be the right phrase. On paper it doesn't shine, but in the air is where it counts.

The fastest Japanese Army fighter was the Frank, when running good. The most often called best fighter was George II, the best B-29 intercepter was Shoki, the most serendipitous mongrel hybrid was, in fact, the KI-100. At one time, the hottest fighter was the KI-61. Pappy said so. Question: what was the nature of the problem in manufacturing DB engines in the first place? I have never even heard any half-decent conjecture.

Why was it called "best Japanese fighter of WW2?"
Speed isn't exactly impressive - Ki84 is faster, maybe also N1K2-J. Is it turning radius? High-altitude performance? Thrust-to-weight?

Woah Mr Wolf! The engine that transformed the Ki61 into the world beating Ki100 was a Bomber engine!...the Mitsubishi Ha 112! The Homare was nowhere near as reliable and not considered for use in the Kawasaki fighter. But it is easy to see how you got them confused...we all do!

It truly was an amazing feat of engineering that Imperial Japan could develop such a fine fighting machine at this stage of the war. She was deployed in February of 1945 at a time when Japanese industry and cities were being pummelled unmercifully by Curtis Lemays B-29 bombers. Joining a Mitsubishi Homare 112 engine with a Kawasaki KI-61 airframe was done by studying blue prints of the Yokasuka D4Y1 torpedoe plane and having help also from the Focke- Wulf staff who married a BMW 801 engine with a slim airframe and developed another fine fighting machine. The Kawasaki KI-100 was truly an outstanding fighter for its time and the pilots praised how easy it was to fly.

Propably the best japanese fighter of WW2