What sets the Rubicon apart from the others? What model should I be looking for?
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Rubicon has Dana 44 axles front and rear with Electronic Lockers F/R & 4.10:1 Gears.
Rubicon has a 4:1 Transfer Case.
All other models have a Dana 30 front and Dana 44 rear and no lockers & Various gear ratio's up to 3.73:1 max.
Non-Rubicon's have a 2.72:1 Transfer Case.
There are a few other differences, but those are the big ones. If you plan on doing any rock crawling you will want the 4:1 TC, if not more, and shorter gears. Once you upgrade to 35"+ tires the non-Rubi gears get pretty worthless and makes the JK difficult on road, especially the auto.
If you are just mudding then the taller TC and gears won't hurt you any, in fact they are better for keeping your wheel speed up to clean out the tires.
*edit* oh yeah electronic swaybar disconnects on the Rubicon as well, as posted above.
The D44 axles are also 30 spline in the non-Rubi and 32 spline in the Rubicon D44's.
Suspension isn't really "beefier", it has gas shocks, but so do the Sahara's, and they will typically get replaced when lifted anyway.