Also, too, he doesn't oversee and sign off on everything that happens at the NSA.
I don't offer that as a defense (except for things that happened before his watch, of course), but while ultimately the man in charge is the man in charge, I think that often criticisms of things which happen during this administration are just heard as criticisms of Obama by people who are, understandably, fans and invested in his success.
The surveillance state, the Pentagon, and, yes, government procurement practices generally are complete clusterfucks. And that's the most innocent observation one can make about them. They're also empires of their own that no one man can change overnight. I'm obviously not someone who thinks Obama's instincts and priorities are always correct, but I also don't think "criticizing the NSA" is necessarily "criticizing Obama."
I'm not absolving management of responsibility, just saying they aren't omnipotent or omniscient either. They don't always know what they should know.