I could be mistaken, but I think John's issues begin and end far beyond the bounds of the Stargate Program, which is one of the things that makes him really interesting to play with in AU 'verses.

You've hit the nail on the head - John desperately, desperately needs to feel like he's doing some good, serving a purpose. Atlantis allowed him to do that; Area 51? Not so much. And I can see him being kept in the dark about the F-302 projects, too, just because he doesn't have the right clearances and it's not 'his' department.