DaveBB,
I'd have to quibble about characterizing the F-111 and F-4 as failures or marginal successes... The F-111 was rightfully rejected by the Navy but it was one hell of a final "century series" cold war fighter-bomber. Not much of a fighter and thankfully not much money was poured into trying to make it one, but it was one hell of a deep strike fighter. Fast as anything else out there with tons of fuel and bombs and, for the time, a superb navigation and targeting system. Even the modern day combat proven F-15E isn't quite the penetration bomber that the F-111 was, due to lack of speed and high-speed endurance.
The F-4... well, the widespread popularity of the model around the world and proven combat results say a lot. And if I recall correctly, the F-4 was originally primarily intended for the Navy and had to be modified for USAF use.
Other aircraft that turned out well only because they were NOT joint programs are the F-16 and F-18. People forget that the prototypes of both the F-16 and F-18 were competing for the same lightweight fighter program. USAF chose the F-16 and the navy realized that the F-18 would, with appropriate design work, make a fine naval fighter.
Now imagine if the F-35 was "usaf only", and the Navy had to run its own fighter program separate from, but loosely based on the technology behind, the F-35? They could have widened/stretched it and given it 2 engines, if the basic model didn't also have to do STOVL for the marines and fit on the little amphib carriers. That could have been a hell of an F-18 successor, a 15% or 20% bigger acft based on F-35 era technology, but with 2 motors and no compromises for USAF or USMC joint requirements. Maybe they could have even made a 2-seat version for precision strike/attack and EW. How do you control your nifty new stealth navy attack drone fleet without a WSO/RIO in the back seat? Not very well, I bet...