A trial costs both sides a lot of time and money. In most cases the defendants really are guilty (they had so much evidence on this guy I'm not sure why he even chose to go trial), the government has a lot of evidence against them and they would receive no benefit from going to trial unless they are being prosecuted under some new theory of liability that they could maybe convince a jury is invalid. Honestly it's surprising the conviction rate is only 95% instead of 99.9%. Federal law enforcement has multi billion dollar budgets, they can issue warrants and subpoenas and wiretaps, they can give "friendly knocks" and threaten people with jail time for not cooperating. How do they ever even lose?
Lack of motivation. Relatively few people on the prosecution side truly care about winning, especially as time passes.
Cases can easily take years, personnel changes ruin everything.
If you have money and aren't accused of anything totally crazy, you can easily completely ruin the governments chances by simply getting a few of the main people involved private sector jobs. This happens every day.
