Interesting, though not terribly surprising. I have never played "Ace Attorney" but this does make some other things I had been wondering about (from books, Anime, etc...) a bit more clear.
That said, there is never going to be such a thing as a "perfect" legal system. Heck, even if we did create a system that was perfect through some kind of psychic precognition or whatever, that in of itself would freak people out. While the point of movies like "Minority Report" was that the system had flawed, even if it worked perfectly it would still scare the bejeezus out of people if something like that could ever be implemented... not to mention other science fiction tropes like "thought police", "psychic detectives", and "brain scans".
Going back to the old days when Dinosaurs walked the earth, and I took Criminal Justice, I basically agree with the maxim that there are basically two types of functional legal systems. There is the kind of system that would rather see a guilty person go free than an innocent go to jail, and the kind of system that would rather see an innocent go to jail than a guilty person go free. There are arguements in favor of both attitudes actually.
Even in the US which is a system where we'd rather see the guilty go free than punish an innocent, we can't even come to an accepted consensus on what is fair. Ask a simple question like "should the law apply equally to everyone?" and people will say "yes" but then inevitably (as I've had demonstrated in class) pretty much everyone will come up with exceptions based on a "free hand" needed for certain jobs, or how rapists and child molesters should be continuously singled out and "punished" through omission even after their sentence, and whatever else.
I think the biggest problem with Japan's system as I was reading it probably isn't the lack of a Jury, but apparently that these Prosecutors don't seem to be in any way accountable to the people themselves. A DA/Prosecutor/State Attorney General gets too 'iffy' or out of control and they can wind up out of a job very quickly. That seems to work fairly well, though admittedly like everything it has a down side: and in the US it's that the pressure to hold office/keep getting re-elected leads to them doing what is popular as opposed to right. To some extent allowing for "mob justice" based on the whims of the people. I look towards the Rodney King thing as an example, whatever you believe about what happened the bottom line is that the officers in question were found innocent, due to a riot they were for all intents and purposes re-tried and found guilty... something that isn't supposed to happen. For that reason alone I consider that one of the greatest failures of the US justice system. While I think we get it right for the most part, I suppose Japan's system makes things like this less likely.