Like we said Lunatik, it's probably just internal politics.
The F-35 can't have a worse RWR system than our current line of fighters and they seem to do a pretty good job of detecting incoming threats.
Also I can't imagine the F-35 not being able to carry at least a pair of AGM-88 HARM missiles internally. At least one. Come on, seriously.
As of stealth capability, I don't think they're pouring this much money into something that's less stealthier than the F-117 and that bird never had any serious issues with penetrating enemy airspace. Yes, one did get shot down over Yugoslavia, but considering how it's never been brought down in any other instance, it could be a fluke.
Maneuverability, range and speed might be factors.
At Mach 1.6, it's not the fastest jet in the world. Its ability to run from unfavorable situations could be limited.
It's got a longer range than the F-16 so I don't think range is much of an issue.
Again, most likely just politics.