The Navy doesn't have a problem with the F-35, it has an A-12 hangover...

via Flight Global...

The CFTs, which Boeing has pitched to potential buyers as part of its Super Hornet international roadmap, would allow the F/A-18E/F to carry more than 13,249l (3,500gal) of additional fuel. "Adding these tanks would make a great deal of sense," says Mark Gunzinger, an airpower analyst at the Center for Strategic and Budgetary Assessments. "The navy really needs to extend the reach of its carrier air wings. Increased range will be needed for potential operations in the Pacific region and elsewhere."
The USN's efforts to add CFTs might be part of the service's plan to hedge its bets in case of further delays to the Lockheed Martin F-35C, or if budgetary pressures force the navy to abandon that variant. "At this point, the F-35C is easily the most troubled variant," says Richard Aboulafia, an analyst at the Teal Group. The USN has always been lukewarm toward the stealthy single-engined fighter even if senior service leaders always publicly profess that the service "needs" the F-35C.
But there are questions as to whether the Super Hornet can support the added weight and drag of the CFTs without seriously impairing its aerodynamic performance. "One problem with CFTs on the F/A-18 is that I'm not really sure it has the power," Aboulafia says. "If they put CFTs on the [Boeing] F-15 and [Lockheed] F-16, they're fast jets. But the Super Hornet is already pretty much slowest in class."

What you're seeing is a US Navy that is taking a traditional jet and attempting to make it fit its needs in the Pacific.

If this was based solely on costs alone it might be seen as a good thing.  But it isn't.

The US Navy is suffering from an A-12 hangover and is unable to move forward because of that planes cancellation.

While other services have been able to move forward after having major procurement items killed the US Navy, in particular the carrier Navy is stuck in a bad place with lingering issues over its future.  Right now you have a couple of different cabals fighting it out trying to determine which way to go.

You have what I call the futurist that support the X-47.  This group is ready to send manned aviation over the side and place most of its marbles in the robotic aircraft camp.  The problem for these people is that the concept has never been tested in denied airspace.  As a matter of fact I've never even heard of UAV's being fought in Red or Green Flag against simulated opposition. If they have been then I would bet that the loss rate was horrendous.  And that's the real issue with UAV's.  The Iranians might not be able to tag them, but most other modern air forces would have a turkey shoot against even advanced UAV's like the X-47.

The F-18 camp has a if it ain't broke don't fix it view.  They will and are seeking to squeeze every ounce of performance, every penny of procurement dollars possible to support their world view that for now the F-18 is good enough.  Problem for this group is that our potential enemies are moving towards high performance stealth airplanes.  Unless a breakthrough has been achieved and AESA or some other sensor is able to detect and track stealth without fail then the issues are obvious.  Note that the F-18 is also the slowest of all the 4th gen fighters and when you add weapons it becomes obvious that this airplane just isn't cut out to fight the next high tech war.

That leaves the F-35 lovers.  The airplane meets (on paper at least) all requirements.  The reason why it isn't globally loved is because of the delays in getting it into service and the cost of the plane.  I blame all three US services for the delay.  Have you taken a serious look at the X-plane and compared it to the production model?  The plane has suffered massive changes...gained a ton of weight...had many new requirements slapped on it...

The F-35 suffers mostly from a clash of the old procurement model meeting a new one.

In the end I predict that the F-35 will be used by the Navy.  At first they will fight, cuss and kick before they get into the stealth game but in the end...after they've gotten slapped around by USAF and Marine Air in war games...they'll be some of the planes biggest boosters.