At a federal level criminal defendants face increased sentences if they do not plea out. Even worse, criminal defendants will get hit with additional charges. So the choice is, either admit guilt, or we will throw every charge we can at you. Due to weakening of double jeopardy laws, defendants often first get prosecuted at a state level and then can face similar charges at a federal level. The system gives too much power to a prosecutor, whose only measure of success is number of convictions, and who will face no penalty for wrongful conviction. Lost evidence is also a problem, but I think it is secondary.