The numbers aren't wrong, though I understand where you're coming from. The accused tends to see better legal representation and experiences more educated judges, but you've been misled if you believe investigations for federal crimes take years. Yes, certain things like murder, conspiracy, large scale fraud, and operating a criminal empire can take years to investigate and years to finish the trial.

But that's not the majority of federal cases. You're looking at a federal prison population where 50% of the inmates are there on drug charges. Those cases happen quickly thanks to the aggressive drug laws on the books. Arguing whether current drug laws are just or not is another argument entirely, though mandatory minimums have placed a good portion of that population there for a long time.

Second to that are weapon and explosive charges, and then immigration. Federal laws make these hard to defend in a federal court. Thing is, as you basically said, you are rarely charged with a federal crime if the evidence isn't clear. Other lesser charges like tax evasion and money laundering have their evidence gathered by the IRS, and it's hard to challenge the numbers they provide.

State and local governments are not that efficient. Public defenders and prosecutors are thrown cases where the evidence is provided by a police agency that will never be as efficient or abide by the law as (most) federal agencies will. Judges are less educated and unwise compared to their federal counterparts, and being paired with a crappy PD and an aggressive prosecutor is a recipe for a "guilty regardless of innocence" case. State conviction rates are lower than federal rates, however, depending on the state you can still see an 85%+ conviction rate. That's a state average. When you break it down to the county level then some might be weighed at 95%. It's never good when you have a prosecutor (or five) that has a 98% conviction rate.

I've seen cases where a defendant has accepted a plea deal before even making it to discovery. I know I've complained a lot about prosecutors, but the detectives in charge of trials are usually the ones that create situations like this. They'll drag their feet and tell the prosecutor the evidence is coming. Pre-trials are pushed further and further back. You'd be surprised how many people who have nothing on them accept a deal because they can't take the stress of going about their lives with the possibility of massive jail or prison time.

State courts may take cases as they come. That doesn't mean they can't continuously delay them.