In the case of USA vs. A Swartz, there were already over a 100 filings and the case had not even gone to trial yet ( http://ia700504.us.archive.org/29/items/gov.uscourts.mad.137... ). All that back and forth requires billable hours from a very pricey attorney, the money adds up very quickly. I do not know enough about the legal system to determine how the discovery/pre-trial motion process could be made more efficient and cheaper for the defendant.
I don't want to take the number at face value because it includes the amount spent by guilty people trying to avoid jail at any cost. Kenneth Lay no doubt spent a pretty penny on his defense.