I know I'm late to this portion of the discussion, but I have some thoughts about this article, based on 2 decades of investigating cases, in multiple US Districts.
First, I have never seen any AUSA willing to charge something unless they were extremely confident it would result in a conviction, if it went to a jury trial. I'm not talking about being confident about 1 or 2 counts, and "iffy" about the rest. Every AUSA I've worked with will only charge a count if they are extremely confident they will get a conviction, at trial, on that individual count.
Second, one of the reasons the conviction rate is so high, is that fed cases are usually filtered at many levels prior to ever charging someone. The agents will decide what to spend their time on, and vet allegations to see if a case merits time investigating. Then their supervisors might also shut them down, because even if the agents want to pursue a case, the supervisors might decide their time is better spent elsewhere. Then depending on the type of case, it might require scrutiny by higher levels of management, before the case can be worked. Then when the case is referred to the US Attorney's Office (USAO), it will be analyzed by an Assistant US Attorney (AUSA), likely both a supervisor, and the AUSA who will actually work the case. Again, depending on the nature of the case, higher levels of supervision in the USAO may also scrutinize the case. Also, depending on the nature of the case, it might even require scrutiny by main DOJ. At any point along the way if someone thinks they won't be able to convince a jury of guilt beyond a reasonable doubt, an individual count, or the entire investigation, whether with regard to a particular suspect, or all suspects, can be shut down.
Third, the author of that article doesn't use the exact terminology, but alludes to what is often referred to as "stacking charges," with this:
"In practice, the way this works is that prosecutors get a hook into someone (for Vickers it was perhaps the sanctions violations) and then go looking for additional charges. Those will be easy to find, and then prosecutors come to the defendant and say, “We have 20 charges against you. Each one is punishable by five years in prison. You can go to trial and risk a 100-year prison term, or you can plead guilty and we’ll ask the judge to let you off with a one-year stay at Club Fed.”
The "stacking charges" complainers, want people to believe an AUSA will have one or two solid counts, and add on several "iffy" charges, just to force a plea deal. See my first point, as, in my experience, AUSAs want every single count to be something they are very confident will result in a conviction. Also, the reality is people often commit multiple crimes. Take a cocaine trafficking conspiracy for example. If a suspect, in the case, is a felon, and possesses a firearm to protect himself while trafficking drugs, the evidence might support a substantive count for possessing cocaine with the intent to distribute, a conspiracy count for participating in the scheme with others, and a count for being a felon in possession of a firearm, along with a count for possession of a firearm in furtherance of a drug trafficking crime. That's not "stacking charges," that's charging all the crimes the AUSA believes the evidence proves. In a narcotics conspiracy case that might be typical for a low level member of the conspiracy. For the higher levels of the conspiracy, financial crimes related to tax evasion, and money laundering might also be charged. That's a just a simple example.
That's not some unfair "stacking of charges," that's charging all the crimes the person commits. No rational person would say the government can only pursue one charge, and give a "free pass," on all the other crimes someone commits.
Next there is claim that 20 counts, each with a 5 year statutory maximum, means the defendant is risking a 100 year prison term. While theoretically possible in some cases, it's not even remotely realistic. Judges generally have discretion to run sentences for various counts either consecutively or concurrently. However, everyone, the AUSAs and defense attorneys know, what a defendant's guideline sentencing range will be, which is rarely the statutory max, and they further know judges rarely run the sentences for all counts consecutively. Defense attorneys are able to give their clients a very realistic estimate of the likely sentences if their client gets convicted at trial, or accepts a plea deal. Part of that will be presenting the plea offer from the government, which likely involves dismissing some counts, resulting in a lower probable sentence. Again, that's not the government getting rid of some "iffy" "stacked charge," that's the nature of any deal. Both sides need to get some benefit. For the government, the expense* (in time and money) of a trial is avoided, and for the defense their client gets a lighter sentence.
* Contrary to popular myth, the government, including the LE agencies, the USAOs, and the Courts, do NOT have unlimited resources.