Criminals should be a tiny group of antisocial people who deserve serious consequences for their serious actions, with law enforcement enforcing a limited set of laws (rape, murder, etc.) universally - going after every criminal that comes to their attention. Fair and understandable.
Back in reality, most of us have probably innocuously violated some federal law already (Silverstein's Three Felonies a Day has been mentioned a bunch - it's a great book.) Even in cases like Swartz's where his violations were arguably intentional rather than accidental, the penalties are completely disproportionate to the action.
In this system, where we're practically all lawbreakers, the government has the discretion to decide exactly whose lives they want to ruin. In the best case they're enforcing the law selectively in line with their best moral judgement - for example, Al Capone. He was generally suspected to be a bad guy, but no one could prove that he committed any sort of real crime - so out of the millions of people that cheat on their taxes every year, the government singled him out to prosecute for tax evasion, and then threw the book at him. Maybe jailing him was a good result, but by selecting one man out of a pool of millions of lawbreakers to go after, the government crossed the line from the rule of law to the rule of man. And think of the result when the government's initial instinct about a person's "good guy" vs. "bad guy" status is wrong!
In this system, the nightmare is the malicious prosecutor, one that's not even attempting to "do what's right" but instead is selecting cases to prosecute for personal motivations - political advancement, personal causes, etc. People who are initially targeted for federal prosecution but somehow 'escape' are frequently recharged for something else - for example, the hapless fuel-cell entrepreneur Krister Evertson. That's what it sounds like happened to Aaron Swartz - thanks to the previous federal investigation into PACER, when he popped up again the federal government was delighted to go after him with both barrels, for reasons having nothing to do with MIT or JSTOR. Even if PACER wasn't an influence, going after Swartz instead of modern Al Capones shows that the arbitrary rule of man we've got in place of a real legal system is working pretty damn poorly.
The way to solve this problem, ultimately, would be to dramatically shrink the size of criminal federal law - ideally by limiting what can be declared criminal in the constitution, since we certainly can't rely on the legislative branch's sense of justice. This will never happen, at least not until this system is torn down and another is constructed (yeah, you scoff, but historically this does happen from time to time). In the meantime, we might as well find legal ways to make being a prosecutor politically unrewarding, and look for incremental reform where we can find it.