The answer to this question
given at the time was:
The JSF Concept Demonstration Program is not meant to be a competitive fly-off. The Boeing JSF X-32 and Lockheed Martin JSF X-35 are not prototypes – they are technology demonstrators, hence the "X" designation, as opposed to the "Y" designation used for aircraft such as the YF-22 and the YF-23 (prototypes for the F-22).
Doesn't explain why the winner became the "F-35" though. This thread may explain why it wasn't the "F-24", however; perhaps that designation was already taken.
Thinking further: You could imagine a scenario where the DOD didn't wish to invite rampant speculation about existence of a missing aircraft if the JSF designation had been announced as "F-25"; remember the fuss when there was a gap between F/A-18 and F-20 (Tigershark)?
So why not leap straight to 35, and leave lots of other handy holes in the system to be filled within the black world? There you go - problem solved
