I spent a lot of brain cycles considering this exact thing last year.   I was so back and forth on the topic, that the decision ended up coming down to price - I found an identically-optioned pair of Rubicon and Mojave trucks headed to a dealer, and chose the Rubi because they'd discount it ~$5k or so and wouldn't deal on the Mojave.  I also know I can't leave well enough alone and the Rubicon has more (easy) modification options down the road.    A couple months later my wife and I made a 2500mi loop trip around NM, UT, CO in it.   In the meantime another jeep-owning friend and I convinced a 3rd buddy to buy and he ended up with a Mojave, and so I've got to spend a wee bit more time with one now.
I think it's very much a "begin with the end in mind" exercise.   What's the end goal here? 
Mojave:
+Advanced suspension in stock form
+Reinforced frame, iron knuckles - durability
- Advanced suspension may limit (or be wasted by) future suspension modifications
+ A bit more front tire clearance out of the gate
- No front locker 
+/- Std. low range T-case 
+/- Cosmetics (Subjective - orange, hood scoop)
- no front swaybar disconnect
- no Diesel option 
+ slightly wider track width, IIRC the oem wheels are spaced a bit wider and may better accommodate going up a diameter (if they're wide enough).
Rubicon:
+Front Locker
+/- 4:1 tcase
+ front swaybar disconnect
+/- softer suspension, but with more modification options down the road
+/- cosmetics (red, vented hood)
+ diesel available (if you want that sort of thing)
- Aluminum knuckles unless you get the diesel
I think the most overlooked, subtle but biggest real difference on the trail is the T-case.  The 4:1is amazing on highly technical rock stuff but is really low, leaving you with a pretty big gap between 4-lo and 4-hi.    This might be further influenced by your transmission choice, with different gearing in the auto (my choice) vs. the manual.  Still, I think the the Mojave's standard case is a PRO for "overland" type camping, mild trail, exploring type stuff.   Not discounting that it was my first trip in a new vehicle so I was feeling it out, but around Moab I found myself in many cases wanting a little lower than 4-hi but annoyed by the super low of 4-lo.  
Beyond that, getting back to the "begin with the end in mind" comment....
Obviously, if you have a strong preference for one use case or the other - desert woops or technical trails - the choice is fairly obvious.
If you plan to leave it mostly mechanically stock, and use it on the road and mild trails - lots to like about the Mojave.   
If you want more reserve capacity for low-speed technical driving, or want to get gnarlier with suspension lift/tire mods in the future, Rubi may be the way to go.