The prosecutor had to dig around to even find a crime with which to charge Aaron. JSTOR, the so-called victim, did not even want to see the prosecution move forward and had to be subpoenaed for evidence against Aaron, with whom they had already settled matters. The prosecutor's case was based on an extremely expansive interpretation of the law, and additional charges were added in retaliation for Aaron's decision to actually exercise his right to a trial.
Basically, this case embodied almost everything that is wrong with the criminal justice system in America.
Nothing. It's exactly how the US works and our legal system is constructed. Until pleas and plea bargaining are (rightfully) considered duress/forced confessions, piling on charges to force a plea is commonplace, and will continue to be commonplace.
The charges themselves are based on law that is rather too harsh in many people's opinion, given the scope and effect of the "crime" itself.
E.g. there's no reason that this should have been a felony, but the option of pleading to something that was a misdemeanor wasn't even available to Aaron here because of the way the law is constructed.
However given the law and the way the legal system works the prosecutor was certainly treating this just like any other CFAA case.
Basically, this case embodied almost everything that is wrong with the criminal justice system in America.