This may be the last message you expected from me, but Obama should pardon Hillary. If Obama does not, Trump should.
Look, I am a FOIA absolutist. Long before it came out that Clinton may have had top secret emails on her home server, I wanted to see her punished for her flouting of public accountability laws. Her whole home-brewed email system was a transparent attempt to evade FOIA, and consistent with her history of attempting to duck transparency (going all the way back to her abortive health care initiative she ran as First Lady). In addition, I have had it up to here with bogus non-profits that pretend to do charity work, but are in fact merely lifestyle and influence maintenance devices for their principals. I would love to see the Clinton Foundation investigated (though market forces may take care of that institution on their own, as it is unlikely donors will be sending much money their way now that the Clintons have no prospect of returning to power).
But the optics, and precedents involved, with a winning candidate's administration criminally prosecuting the election's loser are just terrible. Even if entirely justified, the prosecution smacks of banana republic politics. And even if it were justified, half the country would not see it that way and next time, when the parties are reversed, as sure as the sun rises in the East there will be folks looking to duplicate the prosecution in the other direction.
The rule of law is seldom helped by ignoring wrong-doing, but in this case I will make an exception.
Postscript: By the way, what could be a better political FU than having Trump pardon her? An attempted prosecution could last for years and could lead nowhere. But nothing leaves the impression of "your guilty" like a preemptive pardon (see Richard Nixon). From a political point of view Obama should pardon her just to prevent Trump from doing so and getting credit for being a healer.