The main problem is the Marines wanting a replacement for the Harrier, something that can do STOL/STOVL operations, and that is completely under their control. The JSF was already under development, and the contractors said they could figure out how to make it fit the Marine requirements. What we got was a fighter that can't dogfight, a strike aircraft with a pitifully small payload, and the political impossibility of starting over from scratch.
One of the lessons that came out of this and the Zumwalt-class destroyer programs is that the military should stop trying to cram every feature into a program. While the proliferation of designs led to unwieldy logistics in the 60s, 70s, and 80s, the attempts to simplify everything have resulted in a reduced overall capability and the need to extend the lifetimes of planes the new projects were meant to replace. The F-15 and F-16 will still be around for decades, and may form a larger part of the tactical strike platforms than the USAF would like to admit. The same will probably be the case with the F/A-18E against the Navy's F-35C.
Dedicated designs are the most efficient. Some of them turn out to be spectacular at other jobs. The F-15 was designed with the adage "not a pound for air-to-ground" and yet from it was developed the F-15E Strike Eagle, an extremely effective air-to-ground platform. Hopefully the military is listening when it goes trying to build its next platform, a replacement for the B-1, B-2, and B-52 expected to come online between 2035 and 2045.