Coney,
We're in the same situation, except that I'm the wife and our son is nearly 5. A-dub just got hired by ExpressJet. Our plan for now is to stay in Jax and hope he gets based in IAH because it's only 1 flight away. The other bases would be harder to deal with because getting there/back will be more complicated.
We decided we'd try commuting and see how it goes. If it doesn't work out, we'll re-evaluate the situation and make some changes. It's not like we are locked into anything. And be sure to disucss the situation with your wife; what she's willing to change might suprise you. I know I've met other pilots who never thought about asking their SO's about it, they just made assumptions that turned out to be wrong.
And if your wife is interested, she should join the forums at
http://forums.jetgirls.net/. It's for families of pilots of all types. It's a great support network. Also, I have a blog that I keep about what it's like to be pilot's wife. PM me if you want the address.
Good luck!
Kim