Non-Rubicon TJ's can also have a Dana 35 out back, if you don't order the optional Dana 44. There is also some kind of rocker protection on the Rubicons. 4. 0:1 low range as opposed to 2. 72:1, the Rubicon also has the slip yoke elminator installed from the factory. Axles are geared 4. 10's as opposed to the wrangler which can only go as low as 3. 73(I think this is right). The Dana 44's are also helical gears as opposed to your standard ring and pinion on wranglers.
I've seen some people blow up those front Dana 30's with a stock 4cyl, manual transmission, and 33's playing in mud, personally doesn't give me much confidnece in the axle. Granted they were trying to keep up with guys running 42's or bigger.
Basically to make a wrangler catch up to a Rubicon you have to spend way more than the purchase price of the Rubicon.
I think I've seen suspension kits specifically for the Rubicon, so there might be some kind of difference in the suspension, no difference in price if I remember correctly.
Hope this helps
Tom