I'm a lawyer with some experience in criminal law, and my reading is that the FBI didn't think they could get a conviction on the intent requirement. Most criminal laws require some form of criminal intent in order to get a conviction (the legal term is "mens rea," or "guilty mind"). Criminal intent can include, for example, knowledge and intent, recklessness, and gross negligence. This is why if you purposely swerve your car to hit someone you'll be charged with vehicular homicide if he dies, but if someone runs into the street from between two parked cars and you accidentally hit him, you won't. The statutes at issue here require knowledge and intent or, in one case, gross negligence. And while it's easy to say she was grossly negligent in the colloquial sense, it's harder to get twelve jurors to unanimously say it's beyond a reasonable doubt that she was grossly negligent. Edit 1: I got around to looking at the actual statutes and adjusted the level of mens rea/criminal intent required.
If I were to play mind reader here, I would guess that the FBI's thinking is that if you're going to recommend charges against a major party candidate for president, you'd better be damned sure the grand jury will vote to indict, and that a petit jury will vote to convict. Otherwise it's a massive black eye for the FBI - perhaps the biggest in the history of the agency: they've changed the course of the presidential election only to fail to get a conviction. Comey was focused on the intent requirement during his press conference, so it appears they just didn't think intent would be a slam dunk before the grand jury and, if they vote to indict, the petit jury.
Frankly, this is probably the best result from Trump's perspective. Sanders consistently polls better than Hillary in a one-on-one matchup against Trump, so he's better off facing Hillary, who likely would have had to step aside if the FBI had recommended charges. And there was plenty of red meat in Comey's press conference for the Trump campaign and his super PACs - the linked article itself notes that "Mr. Comey delivered what amounted to an extraordinary public tongue-lashing." I guarantee you'll see attack ads playing parts of Comey's statement ad nauseum. So Trump supporters shouldn't be too disappointed by today's events. Edit 2: Yes, I know that Hillary is a known commodity, while Sanders's poll numbers might drop if he were the candidate and the Republicans turned their fire on him. The point is well taken.