If somebody who didn't do anything bad is suspected of breaking the law, that somebody will have to be investigated, and is well advised to defend himself or herself.
By all means let them provide the investigators with information, but that shouldn't require being physically present in a courtroom at a specified time.
Since you're trying to establish good or bad here rather than legal or illegal, you need to do a lot of investigation and consideration, and get the facts nailed down to make a good decision. That's going to occupy the defendant for some time.
I don't see why it has to. A defendant should only be tried if it is clear they did something wrong.
I'm not suggesting that defendants won't end up spending ANY time resolving issues that come up. However, the system needs to be optimized for their convenience, not the convenience of the court. Also, investigators should be personally liable if they contribute to an investigation that comes to an incorrect conclusion.
I'm fairly confident that this will GREATLY increase the costs of running the courts, but I don't think that jailing the most accused per dollar spent should really be a metric we use to evaluate the performance of the "justice" system.