The plea bargain is the result of a couple of forces in the criminal justice system:
1) The vast majority of people accused are, factually, guilty. You hear about the edge cases in the news where someone is convicted on flimsy evidence, but for each one of those there are a dozen people who did what they are accused of doing, and the police have ample proof. They blew a 0.20 on the breathalyzer while driving, they were found with a pound of cocaine in their trunk, the police were called to the scene while they were beating up their wife, etc. The premise of plea bargaining is that it makes sense to allow those people to plead guilty and save the public the expense of a trial.
2) There are too many criminals and not enough public defenders and prosecutors. If 90% of cases didn't end in plea bargains, the system couldn't process all the accused. Part of the problem is that we've criminalized too much behavior--thank the drug war for that. But it's not just drugs. Large and medium-sized U.S. cities have 5-20x the murder rate of major European cities. New York, the safest big city in the U.S., had 5.6 murders per 100,000, while comparably-sized London has 1.6. Chicago is at 18.5 versus comparably-sized Madrid at 1.0 per 100,000. There is something severely dysfunctional in the social fabric of the U.S. that necessitates a much more aggressive policing and prosecution function.
I think the original justification of plea bargaining (1), has been severely distorted in light of the pressures created by (2). It makes sense to a degree, but it has been stretched, often out of necessity, far beyond reasonableness.