I have owned a 2.6 5spd Trooper for 13 years. I've always been convinced that's the best combination. Until a year ago, when I bought a 2.8 5spd Trooper. Now I'm not so sure. Having driven both extensively and compared performance, here's what I find:

Better fuel economy can be realized with the 2.6--22 mpg highway when driven reasonably, the 2.8 has never gotten more than 20; in low speed off-road performance, the 2.8 is preferrable--it will climb my steep driveway at 400 rpm while the 2.6 doesn't like to run that slowly.

If you envision some day wanting enough power to compete in freeway traffic, or to pull a trailer, the 2.8 can be greatly improved by replacement with a 3.4. You'd have to do a lot of tweaking on the 2.6 to get as much power out of it, and then you'd lose some reliability.

As Jim noted, there really isn't much difference between the two engines. If you don't intend to make any modifications, either one is acceptable, with a nod to the 2.6 for better economy.