I have both (well, my wife has the Rubicon, and I have an 05 X). Both are stock, but even so, both can get us to all sorts of places. Still, this summer we left the Rubicon at home and took the Xterra to Moab. Here's why:

-The X holds way, way more gear, and you can secure the gear better using the utilitrack.

-My stock 05 X has better ground clearance than a stock Rubicon (go to rubiconownersforum.com and read up on the low-hanging transfer case skidplate, a.k.a. the "shovel.") In the Rubi, we're always banging something. Once I get sliders for the X, we'll be set.

-The X gets better gas mileage and has a bigger gas tank, which gives it a much longer range for backcountry expeditions.

-The X got us to Moab comfortably. (A Rubicon doesn't need a big gas tank, because no one would want to ride in one long distance.)

Now, having said that, the Rubi is a great Jeep. At 20,000 miles it hasn't had a single problem (and no squeeks, unlike the X). It's articulation is better, and 4lo in the Rubi is just plain awesome. Comparing two stock vehicles, my wife's Rubicon can out-crawl my Xterra. It's also nice to be able to put the top down on a nice day.

But the Xterra offers so much more if you're into more than just rock-crawling. We like to hike, bike, and camp in the backcountry, and so we use the X as our expeditionary vehicle. The Rubi gets used for short day trips to the mountains and (ironically) whenever we drive downtown (it's smaller and easier to park).