I've always thought of the FJC as a very 'specialized' vehicle and certainly "out of the box" it's more off road capable just because it has a shorter wheelbase, smaller approach/departure angles, and better ground clearance. Also available with a locker in all years and IMO benefits from having a by-God 4wd shifter knob instead of the stupid little dial we got on the T4R
Having said that, while the FJC is better at pure off roading, it pretty much sucks compared to a T4R at anything else. Visibility is terrible, it only has two windows that you can open with the touch of a button vs. 5 on the 4runner, rear seat is pretty much useless for adults, and storage capacity is less. Also smaller fuel tank + bigger tires = sucky, sucky range (last year I went off roading with a guy who had a nicely built FJC on 35's. He told me his range between fuel-ups was a little over 200 miles. On my T4R I can typically go over 400 on the highway.)
If "off roading" is all you do, then an FJC might work for you but if you need a vehicle that can do a little bit of everything - drive you to work, take the wife out for a nice dinner, bring home a load of lumber from Home Depot, take the kids to school, etc, then a 4runner is probably a better choice.
To put it another way, the 4runner is the classic "jack of all trades and master of none." What's interesting is that the 4runner's worst shortcomings (approach/departure angles and low ground clearance) can easily be fixed with an aftermarket lift and an aftermarket bumper. But many of the FJC's weaknesses - visibility, access, and short range - cannot be fixed at all or can only be fixed with very expensive measures.