If you are looking for a hard-core rock-crawling trail rig, then go with the shorter-wheelbase vehicle.
If you spend your off-road time mostly on dirt roads that aren't super-narrow and super-tight, then the Unlimited's longer wheelbase will not hamper you. In fact, the longer wheelbase is mostly an improvement on the Jeep chassis... better ride, better handling, better stability, more cargo room. This is the same wheelbase that the Scrambler was built on, and improves everything about the Jeep performance except turning radius.
If you've got around $35,000 to spend on a vehicle, there's a company in Tennessee that will modify your Jeep to a longer wheelbase and put four doors on it. They often have new rigs sitting around (they buy brand-new vehicles and modify them and sell them) and many Jeep dealers nationwide carry these modified Wranglers and offer a full warranty on them.
I have an '84 CJ-7 and an '04 Dodge Dakota. I may very well be tempted to get rid of the CJ and get one of these Unlimiteds in a few years, especially with the Rubicon package.