It's quite easy to calculate the likely sentence. The Federal Sentencing Guidelines provide for a base level of 6, plus an 18 step increase for fraud between $2,500,000 and $7,000,000. The sentencing range at this level assuming no criminal history is 57-71 months. Expect supervised release (no computers) for three years. The fine would be up to the sentencing judge within statutory limits. The government estimated the value of the JStor documents at $5 million. Even if the government's estimate was exaggerated, the documents were worth something--and this figure would drive the sentence to be imposed. The judge could also depart upward based on aggravating factors such as PACER and a lack of remorse. Swartz faced with no good choices. When he did not take the offered plea, they superseded and racheted up the counts. The number of counts doesn't really matter for Guidelines purposes but there is always the risk that the sentencing judge could impose the sentences for each count consecutively.
My guess is that Heyman/Ortiz really didn't want to prosecute the case, afraid that it would become a political hot potato and controversial. They made him what they considered a reasonable offer in September--7 to 8 months federal prison, a fine (amount unknown) and two-three years of supervised release. The kicker is that he could not use computers until supervised release was finished. So for a decade or so, he would be cut off from the digital world entirely.
(There are various reports about these negotiations but I have not seen an offer letter.)
We know that Swartz did not accept the offer. What happened next is what prosecutors do in all sorts of cases: they superseded, that is, replaced the indictment with a new one, adding new charges and new counts. Perhaps they withdrew their plea offer as well, or put a deadline on acceptance.
With a trial date of this week, and advice from his lawyers that he very well could lose (whatever the facts, the hiding his face with a mask would be a prominent feature of the trial, and mummery by the prosecutors just as the glove in the OJ case).
I do not know what his attorneys told him; but from their pleadings they seem to be competent, professional federal defense attorneys, so they would have told him realistically what his chances were. Criminal defendants in these circumstances often take very drastic action.
Someone was pressing this case. It could have been Ortiz. It could have been the case agent. It could have been Heyman. In state court a case like this would almost certainly have resulted in probation. Someone, somewhere wanted Swartz' head on their pike.