The charges weren't ridiculous. If Aaron wanted to avoid the trial he could simply have avoided repeatedly breaking into MIT's open network to access JSTOR. The charges (even the amended ones) were approved by a grand jury. The prosecutors were never pushing for 50 years in prison.
See, this is all part of what I complained about in my other comment about prevarication.
But either way, the point is kind of moot. Aaron chose to be in that situation, they didn't change the legal code just to suit him. Taking the plea would have been the smart thing but he was never under any obligation, as the sentence he would get in a jury trial would be based on the Federal sentencing guidelines (and his expensive attorneys could tell him that too).
Regarding the Sixth Amendment, plea bargaining is one of the tools used to ensure that those who do need jury trials have a chance at getting them expeditiously (or do you really think that Google really has a 5GB hard disk partition sets aside for everyone with a GMail account?).