Ok, so I actually have an Xterra S, an FJ Team Trails and a JK (sadly, the 3.8L). Here are my thoughts:
The Xterra is definitely the most practical vehicle. The motor is great, the transmission is ok and it's great around town and excellent on the highways (except that the stock gearing sucks for bigger tires). Off-road (mine has 32's and a 2" lift) it's ok. It was the first vehicle I off-roaded and while it does alright it doesn't have the same chops as the FJ or the Jeep. It hangs with the FJ for the most part, it just has to work harder. That said, it's still pretty decent and has by far the most practical features. Also, after 120K miles it's been bulletproof reliable, even better than my 2 year old FJ.
With the FJ I already knew I wanted the locker so I got the Trail Teams. The visibility blows. The rear doors are terrible and it has no more space than the Xterra even though it looks bigger. Thing is, completely stock it will out-wheel my 2" lifted Xterra (even without using the locker or A-TRAC). Still pretty good around town. My wife hates it though and refuses to drive it preferring the Xterra.
The JK is fantastic off-road. Mine has a 2.5" lift and 35s and it is in a completely different league than the other two (especially on the rocks or harder trails). In fact, my buddy sold his modded FJ and bought a Rubicon (now with a 3.5" lift and 35's) after wheeling with me. Here's the downside though, it completely sucks on-road. Driving it on a road trip makes me want to flip it over and pee on it. It's loud, loose, can barely get out of its own way up hills with the 3.8L (yes, it's re-geared to 4.88) and has by far the crappiest build quality of the three. It's just embarrassing how sh!tty that thing is built. Still, the basic mechanics are solid and it won't quit running or strand you. It can also take a heck of a beating off-road and comes apart like it's made of Legos. Aftermarket support is just amazing. You can pick up spare axles at Walgreens (well... not quite). If it died on me today, I'd go out and get another one tomorrow. It's that much fun off-road. The new 3.6L JKU still drives like crap and is still loud, but at least the interior is nicer and it can make it up a hill without running out of steam. My buddy loves his.
So where does that leave us? Well, my Xterra is a bit long in the tooth and my wife (after test driving a Grand Cherokee and 4Runner) has decided that she just wants another Xterra. After having done this once already we'll be getting her a Pro4X for the gearing and locker. She knows she wants a 2.5" lift with 33s and for most trails, that'll do just fine. Plus, it's a hell of a lot nicer to drive to the trail.
My vote, spring for the Pro4X if you can afford it, even if you know you're going to dump the suspension. The M226 and e-locker are worth it and they're hard to find and pricey when you do.