This is a long, sad story. To sum it up, during the mid-2000s, the watch-word in Pentagon acquisition was "transformationalism." Transformation, driven from the top down by Rumsfeld and the JCS, led the DoD to make a number of questionable decisions with a number of major new programs, resulting in the incorporation of very new and unproven technology that promised to significantly improve the efficiency and capability of the associated weapon/ship/airplane. In the case of the Ford, the electromagnetic catapult and arresting gear were supposed to improve the sortie rate while at the same time reducing maintenance (and hence lifecycle) costs. Ultimately, this policy of pinning hopes on unproven technology is biting us in the aft end; see also the DDG-1000, the LCS, and the F-35.
Oh, and if you think the Navy is bad, take a look at the Air Force or Army aquisition track record some time!