While I haven't purchased my Jeep yet (2 weeks out), I am in much the same position as you regarding which model to get. Like you, I was sure I was going to get a 2DR when I started this process. But after reading stuff here and at another forum, I've come to the decision that the 4DR is the way I'm going to go. Here are some of the reasons that I've decided on and that others have tossed my way:
If you have kids or are going to have kids, the 4DR is easier to deal with car seats and such than the 2DR.
If you're going to be wheeling tight, tough trails with a lot of sharp crests then the 2DR is probably more what you want.
If you want more stability and to be more able to handle steep inclines going up and coming down, the 4DR is more capable and stable.
If you don't want to spend as much money over the course of the Jeep's lifetime, get the 2DR. Alot of mods are more expensive for the 4DR.
Obviously the 4DR has more cargo room than the 2DR but neither is going to haul a mattress or a couch in the back...
It really just comes down to what you need it to do and what you want it to do. I'd just sit down and seriously think about what you want out of a Jeep and go with what that tells you. You know better than anyone here what your needs are. Will it be your DD (daily driver) or is going to be just a trail machine? Hope this helps a little bit. And good luck in Afghanistan, man. Come home safely... And oh yeah... thanks.
But I do kinda wish now I would have gotten a 4dr but I'm not worried, has room for the wife and the dog.
And one other thing that I've read a couple times in both the forums I frequent... I've never seen anyone who bought the 4DR say "Damn, I wish I'd bought the 2DR." Can't say the same about the 2DR...