I won't lie, I am a Toyota Guy. But a '96 Jeep XJ is one of only two non-Toyotas that has been in my garage and driveway in the past 10 years. The first was a '96 Jeep Grand Cherokee (limited?). This was my then girlfriend/soon-to-be wife's car. It had all the bells and whistles. It had power and comfort but the reliability sucked! Electrical problem after electrical problem due to all of those bells and whistles.
We sold it and bought a '97 4Runner Limited. It doesn't quite have all the bells and whistles; but, it did come with a leather interior and a rear selectable locking differential. I have put on an Old Man Emu Suspension and some 265/75R16 tires (could have gone up a size but it sees rare trail use) and couldn't be happier. The 4runner is quite capable on mild to medium trails (did I mention the factory rear locker?), And is reliable and comfortable to boot.
When I was helping the kid look for a vehicle I looked for another 4Runner. The only problem was that they were a bit out of his price range. I always liked the simplicity of the Jeep XJ's, as well as their price. Besides; in my opinion, the straight six motors are the only Chrysler product built for longjevity other than their diesels.
Now the comparison. I will say that I do all of my own work and haven't had to have a shop do work for me in the last decade. I have worked on both of these vehicles and installed similar modifications to both. Both vehicles have similar mileage, have an automatic transmission and are both 6-cylinders (3.4 liter for the Toyota and 4.0 liter for the Jeep).
POWER: The Jeep definitely feels more powerful. In the Toyota you have to manually downshift the auto tranny in order to keep it in it's powerband when in the mountains. This is not a problem, but it is annoying. I have driven my sister's 5-speed manual version of the same year 4Runner and it feels way peppier, even about the same as the Kid's XJ with the auto. But the seat of the pants performance goes to the XJ.
Results: XJ-1, 4Runner-0.
RELIABILITY: Both motors seem to run forever, with many examples of both going into the 300,000 mile land. Transmissions I'm not sure of; but, both the XJ and 4Runner are approaching 200,000 miles with no tranny issues. The XJ is definitely easier to work on as there is more room under the hood, but, both of these rigs are pretty reliable so that is a moot point.
Results: XJ-1/2 for ease of accessability, 4Runner-0.
COMFORT and FIT & FINISH: The XJ is definitely louder and doesn't seem to be as solid. The body on frame construction of the 4Runner actually makes it feel more solid. The unit-body construction of the XJ just doesn't stand up as well to the miles, especially if used off-road. This can be seen when closing the doors of the two vehicles. The 4Runner doors still close like new while you have to give it "a little extra" when closing the XJ's doors. I have also had troubles with all of the door electrics (locks & windows) on the XJ, not at all on the 4Runner. Comfort-wise; I like them both. I wouldn't hesitate to take either and drive across country, I feel that either would be equally comfortable, but the XJ is definitely noisier. The 4Runner is also a bit roomier.
Results: XJ-0, 4Runner-1
OFFROAD: We'll start simply; the 4Runner came with tow hook points, the XJ did not. The XJ comes with an open or limited slip equipt DANA 35 or Mopar axle (with a DANA 44 as an option in some years)in the rear end. The 4Runner comes with a Toyota 8" axle with the option of having a selectable locking differential. I'll take the Toyota 8" for its strength and light weight over both of the stock XJ rear axles. I would even select it over the DANA 44 due to the ease of the dropout differential for maintenance and potential re-gear purposes.
The 4Runner has front IFS while XJ has a front solid axle. I wouldn't consider one stronger than the other as the XJ comes stock with a DANA 30 (one of the weaker solid axle configurations).
The XJ can fit 29" tires stock while the 4Runner can fit 32" tires. A 2" lift will get 33's under a 4Runner while it will take 4.5" or 3" and some decent trimming to fit 33's under an XJ. The 4Runner is much easier and cheaper to lift properly. I put a 2 inch Old Man Emu lift on the 4Runner with no negative effects whatsoever. Even when I do wear out parts (cv axles and ball joints) they are relatively easy to replace. I put a 3 inch lift on the XJ and it just brought all of the worn out parts to the surface in the form of Death Wobble. While trying to cure this problem I consulted many websites claiming to be Gods in the realm of curing death wobble, I also consulted a few "professional" mechanics and they all said the same thing: "This should cure it." Long story short, the XJ now has new front u-joints and unit bearings, new lower control arms, and every moving part in the steering system has been replaced. What started out as a basic $600 suspension lift turned into a $1,500 fiasco of chasing down worn parts in order to get rid of "Death Wobble". Good thing I was able to do the work myself or it would have cost way more $$$.
After both trucks were lifted and riding on comparable sized tires (XJ-31's, Runner-32's) the $runner road better and went farther with its rear locker.
Results: XJ-0, 4Runner-2. In this realm I am giving the 4Runner an extra point for the simple fact that it was relatively easy to modify without causing a daisy chain of other issues.
FINAL SCORE: XJ - 1 1/2, 4Runner - 3
I tried to keep this comparison as un-biased as possible as I really like both vehicles (especially now that the XJ is sorted out). I already told the Kid that if he ever wants to sell the XJ that I have first dibs. But the way that I see it is that; the 4Runner may be more expensive initially but it is cheaper in the long run to modify into a mild/medium duty trail rig (especially if you find one with the factory locker), and it is a much more solid starting point to build off of.
Either will do what you want quite well. Its just a matter of what your priorities are before you start building.
For reference purposes; my XJ:
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And the 4Runner: