To Answer your question you would really need to be more specific to the ty;e of off roading that you do..and I do agree that Jeeps should be PURE...with jeep components.
The 2.5L in line 4 has a few things going for it that the 6 in line lacks.
1. Lighter overall weight essentially 50% less compared to the 6 in line, yes the power that you can derive from the 6 in line is awesome but often the case in off roading, its not all about power..the 2.5 will give you finesse with the lighter overall weight.
2. Running at optimal engine speeds...with less power, you will need to use the power band better thus creating a more informed and detailed driving experience.
3. Less and easier maintenance over all,Less components to change (plugs, cables etc), more room to work as its not as tight. Less Oil during oil change...less injectors if they screw up to replace...
4. Better overall torque for the engine size (do the ratio...).
5. Room to mount extra batteries in the engine bay...for the winch and other accessories.
6. Comes with a 5 speed manual... more flexible and dependable compared to the auto box normally offered with the 4.0 6.
7. More power/ torque can be realized with a gearing change...either at the transfer case or axles...or both if you wish to get super low lows..
Now with that out of the way... the 6 in line 4.0 will be great IF offered with a 5 speed manual... If you lower the ratios, itll literally climb up walls...great power, great torque and superb engine braking but...heavier, more cost and difficulty in maintenance ...
The decision is up to you as both will return approximately the same gas mileage (well the 2.5L 4 will be excellent at lower speed cruising...).
Jeepers in Malaysia, Off Roading with a 94' 2.5L XJ74