How good is the legal knowledge system?

In a post yesterday I wrote about the way scientists seek to validate hypotheses by finding experiments that might disprove them. If scientists find many hypotheses that follow from a theory and are unable to find evidence that any of them are false, then the confidence in the theory increases. Moreover, scientists replicate each other's work to assure that no errors creep in, and their work is subject to peer review.

I recently heard a very experienced FBI agent discuss how he and a task force he had led conducted a major investigation. I suppose that like all mystery readers, I recognize the detective looks for motive, means and opportunity. I also know the distinction between a "person of interest" and the "suspect", where the law enforcement officers restrict the use of the term "suspect" to those believed to be more likely to have committed the crime.

In the case being described there were apparently a couple of thousand suspects, all of whom could have had motive, means and opportunity.

The FBI agent said that, on the basis of analysis provided by an informant, he became convinced that a specific suspect was indeed the guilty man. At that point, the investigation was transformed in character, and the task force concentrated on finding evidence that would stand up in court to convict that one suspect. I don't see a better alternative, but there is something suspect about an investigation that seeks evidence to demonstrate a preconceive idea.

The protection -- in theory -- in our legal system is that there is an adversarial process in which lawyers for the prosecution and defense both have full access to all the evidence that has been collected by law enforcement. The defense lawyer can also develop and present independent evidence supporting the innocence of his client. Finally, a defendant is not to be convicted of a crime unless guilt is proven beyond a reasonable doubt, as determined in a fair trial.

In the example given by the FBI agent, justice was probably done. Still, one wonders if the defense could muster resources comparable to those of the government's task force, and whether judgement of the existence of reasonable doubt is always adequate.

Are there cases when an innocent person accepts a guilty plea to a lesser charge in order to avoid a trial that he/she can not afford to lose, and can not afford to get the best defense?

The legal system I suppose provides "good enough" decisions on guilt, but the epistemology is not as strong in my opinion as that of the scientific system.