A major part of the loss was that, in lieu of set performance parameters, the DOD had required "that the prototypes actually deliver the performance that the contractor's detailed estimates promise".
In other words, the winner would be whomever's aircraft performed most closely to what they designed it to do.
LM's X-35 met every estimate of performance, and even beat a few - Boeing's X-32 failed to meet Boeing's estimates on low-speed stability in turbulence (utterly vital for carrier landings) as well as in a couple of other areas - it was this that caused Boeing to come up with the proposed redesign with horizontal stabilizers... the Navy had NOT changed the stability requirements, Boeing had overestimated the stability of their design.