Desert Storm air commander, retired General Chuck Horner, makes some very good points as to why we should continue to fund the F136 alternate engine, though the obvious caveat is that he is consulting with GE, who is a part of the F136 team.
Basically, he recites a litany of problems, both from when he was commanding squadrons, and issues with the Saudi Air Force, where the Pratt & Whitney was unresponsive to customer concerns, and their F100 engine was unreliable and over priced, and whenever the competing GE F110 came up, the problems got fixed.
I recall reading about problems with the engine, and how it led to the USAF to fund development of the F110, then called the F101-DFE (Derivative Fighter Engine).
There were problems with reliability, price, and support that were fixed very quickly once there was a competitor on the horizon.
It appears to me that the F135 engine for the JSF is headed down the same path, we have P&W going though a number of cost cutting initiatives, promising that the engine will fall in price, while the manufacturer is saying that the cost savings as production ramps up may not meet expectations.
Much of the fair back from the Pentagon is, I think directed about getting copies of the F-35 JSF made now, and to hell with future operating costs.
The budget item for continuing development this year is small, about ½ billion, or less than the cost of 3 full aircraft, and promises real savings, and performance improvements, in the future.
BTW, as to nonsensical arguments against the F136 engine, we have CNO Gary Roughead saying that having two engines would be too much of a burden on a carrier, despite the fact that just for the fighters, there were 4 separate engines in the 1990s on carriers, the F404 for the F/A-18 C/D, the F414 for the F/A-18 E/F, the TF30 for the F-14 A, and the F110 for the F-14 D.
Additionally, the S-3 was still being deployed with the TF34 engine.
By the time that the F-35 enters naval service, there would be two types of fighters on deck, and either 2 or 3 engines, which would be a lower logistical load.