My theory for this is that it was a crippled in an attempt a futile effort to protect the F-22 purchase.

Well, it now appears that the weapons bay is being modify to fix this shortcoming: (It still is an over priced and under performing platform though)

Lockheed Martin will modify the F-35 weapons bay to accommodate a very long-range, anti-radiation missile and support a potential future upgrade to carry up to six air-to-air missiles internally, a source close to the program says.

………

The contract announcement released by the Pentagon specifically calls for altering the portion of the Station 425 bulkhead inside the weapons to carry “aft heavy weaponry.”

A source close to the program says the weapon involved in the modification program is the Navy’s Advanced Anti-Radiation Guided Missile-Extended Range (AARGM-ER).

………

The modification to Station 425 also will allow the F-35 to carry six AIM-120 missiles internally, the source says.

Lockheed has proposed the so-called “Sidekick” modification to increase the F-35’s internal load-out from four to six air-to-air missiles.

Still a misbegotten waste of resources though.