I'm outside of Savannah. And, unfortunately, yes, I would feel that way even with the APs. I just would not have a good time there with three to run after and try to keep happy. Three in my house or around town is no problem. Three at the grandparents, siblings ball games, and stuff like that, I can manage, but three at an amusement park - no way! No matter how good they are, kids are kids and they are going to get excited.
My husband and I often take a subset of the kids on certain adventures. Makes them feel special and we make sure that everyone eventually gets their turn. In fact, in 2003, I will be taking my then 11yo son to Europe - just the two of us, then my daughter when she is 11, etc... That being said, taking two is going to be more difficult, because whoever doesn't get to go it really going to feel left out unless you play it just right. Maybe take the middle child since they alway have to be the middle child and make your husband promise to do something amazing with the oldest while you are gone. I agree that will be hard.
So, if it were me, I would probably just take the 2 year old. I got away with just taking my youngest to Epcot when he was two and it was a lot of fun. Of course, my husband was taking the other two to Seaworld, so there were no hurt feelings. (It was the day after our cruise and we had APs to Seaworld, but I didn't want to go again, so paid for a single day to EPCOT and the little guy was free.) I don't need help with him when I have him on his own. Think how easy it would be - just the two of you! It would be an easy sell since he missed the last trip - he'd eat free at buffets (I took mine to Akershus - great!) thus lowering your expenses even more. I could go on.
But, I think it sounds like you are strongly leaning towards going and taking all three, so for goodness sakes order some matching t-shirts from Lands End or something so that you can keep your eye on them all.