Actually, with her being active duty Air Force, you are in a slightly better position to get majority of the custody.
Research some, because I think it could work in your favor. I think.
To echo what Aran is saying, I'm not quite sure if the Air Force is different, but in the Army we're on a pretty hefty rotation cycle; IE deployment could come up any time. With her being a single parent, that means your kids would have to be uprooted at a moment's notice, and I imagine you could pitch it at a judge that you definately had the more stable lifestyle. Plus if she has to go to basic for two months or so, plus MOS training, she'd be canned from being a parental figure for a while anyway. I'd think a lawyer would definately want to incorporate that into your argument for custody.