Oh no another short arm vs long arm post.
Ill give you some things Ive learned from reading multiple long arm vs short arm threads. Problem with long arms is that the control arms can get hung up in rocks. I read some old posts with pictures of jerry's old TJ getting hung up on some large rocks because of his long arms. The upside is that you can go with lifts larger then 4.5" without getting extreme control arm angles like you might get with short arms. Now most people think that longer control arms equals longer travel, which is not necissarly true. The longer control arms allow the suspension to cycle freely, it is however the shock absorbers that determine your vertical wheel travel. If you throw the same shocks off a long arm onto a short arm you would get the same travel. However the short arms might start to bind before they reach full travel. A lot of this type of binding can be reduced with control arm joints like the johnny(however you spell it) joints.
My suggestion is, if you are going to stick with 4" or less of lift then stay with short arm. A short arm lifted jeep is just as capable of a offroad machine as a long arm lift jeep. From what I have read on the forums, anything more then 4" of lift is unnecissary. If you understand suspension geometry then I would suggest doing a custom mid arm build, its in between a short arm and a long arm and is probably going to be the best option down the road, I know I will be doing that. If I missed something or said something that was false let me know!