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The first thing you must ask yourself is what do you want to do with your Jeep. Will this be your daily driver? Do you plan on doing some off-roading? If so, how much and how severe? How big do you want your tires/wheels to be? What is the weather like where you will be driving this?
All of this should drive what options you get on your Jeep. I ordered the factory ABS, and I am happy with it. But there are some things to keep in mind.
The factory ABS will preclude you from ordering the larger wheel package. This by itself is not a problem, because you can upgrade your tires and wheels later. I've spoken to a few other people, dealership included, and they all agree that getting bigger tires/wheels will not affect the ABS.
However, ordering the ABS package will also prevent you from getting the Dana44 axle. The Dana35 is what you'll get. This is a fine axle, but you should not go bigger than 33inch tires with this axle, as you are then putting extra strain on them which could cause failure. Don't get scared off the Dana35, though, for all on-pavement, and moderate (not extreme rock-crawling) off-roading, it will be just fine.
Finally, on every vehicle with ABS, the stopping distance is actually a little longer than without. This can be especially unnerving if you have to slam on your brakes on dirt, gravel, or snow. You will remain in control of the vehicle and not lock up your tires, but the stopping distance will be a little longer.
Sorry this is so long, and I hope this helps. Another linke to get some more ABS specific info is http://http://4x4abc.com/4WD101/ABS_offroad.html although that guy doesn't seem to be in favor of ABS on an off-road vehicle.
PS--you should also get the TRAC-LOK feature, unless you plan on adding after-market lockers.