I was a part of the group that did the second engine study to defend continuing the funding for the F136. Since it was cancelled, I'd expect GE to continue funding it internally and when the F135 can't do the job, they show up with an engine that costs significantly more than it would otherwise and they've got Uncle Sam by the balls.
I would actually argue that it's not an R&D problem but rather a requirements problem as well as a military acquisition problem. The former is largely due to the VTOL requirements that the Marine Corps want is largely incompatible with the Navy and Air Force requirements. The problem is that the Marines needed a replacement aircraft and Congress wouldn't approve two aircraft programs so they tagged along. The latter is a far bigger problem in that Congress dictates what systems the military get, which is why we're making tanks that we don't need and sending them directly to the Boneyard.
I personally think the military should be able to establish their own priorities and initiate weapons programs as needed subject to review from Congress. Congress could then insist that the military defend their position but they would not be able to force systems on the military that are unwanted or unneeded.