[polishTar]

Speaking as a complete non-expert, I don't find that a satisfactory/comforting answer.

Just a quick google search shows prosecutors in the US also selectively choose which cases to prosecute (it appears there are around 4x as many cases get dismissed than go all the way to a jury trial), but nonetheless there are many meritless cases that do somehow make it to trial anyways.

I could accept that Japanese prosecutors are a bit better at filtering, but a 99.3% conviction rate does not seem right.

[midoridensha]

Why not? You'd prefer the prosecutors to waste their time trying to prosecute cases where they're most likely to lose? Instead, they either drop those cases, or try to arrange some other settlement before getting to trial.

There's many things seriously wrong with the Japanese judicial system, but this isn't one of them.