There are a lot of pro-and-con arguments about charge bargaining (determining by negotation before trial what charges will be filed) and plea bargaining (determining by negotiation before trial what charges will be pleaded guilty to, to minimize the uncertainty of BOTH sides about the result at trial). Yes, in general the defense bar would like a world in which fewer charges can be brought, because there are fewer crimes defined by statute, and pleas of guilty are less costly, because fewer charges result in severe sentences. The criminal prosecution bar would like a world in which charges and pleas reflect the general reality of who is causing societal harm (as society currently defines that) without massively burdensome trials. The general public just want to do what they feel is right, untroubled by people they think are wrong-doers (to them).
The Economist, a publication I generally like to read (I subscribe to the print edition) tends to take a position that "decriminalization" (their word choice is not usually "legalization") of many currently illegal drugs would be a helpful social policy around the world. That may be. Richard Branson's blog post "Time to end the war on drugs" from a little more than a year ago about Portugal
http://www.virgin.com/richard-branson/blog/time-to-end-the-w...
suggests that Portugal's policy of decriminalization with administratively mandatory treatment
http://www.rollingstone.com/culture/lists/top-10-marijuana-m...
reduces drug use in Portugal while reducing burden on the criminal justice system.
Coming back to the submitted article's last suggestion, "A more sensible idea would be to require the state to provide the defence with all its evidence—particularly any exculpatory evidence—during the plea process, rather than simply during or before trial," it is mandatory in the United States for the prosecution to share its evidence with the defense before trial. Failure to do that can result in the reversal of a conviction. But a defendant like Aaron Swartz was able to lawyer up enough, and do enough pretrial investigation, to be quite aware of what exculpatory evidence was on his side. He had other channels for protesting about the issues that concerned him, and he had the choice before him of doing what Thoreau, Gandhi, and King did of protesting a law he thought was unjust by publicly accepting imprisonment for it after a trial. Even after criminal law reform, there are still going to be people who think that their approach to solving personal problems shouldn't be subject to criminal sanctions, with laws still being on the books against their overt behavior. This problem of many possible charges and a drive on both sides in the criminal justice system to bargain can be reduced, but it cannot be eliminated, maybe especially in cases like that of Aaron Swartz.