First, welcome to ExPo! Jump on in the water is warm! :elkgrin:
Which is a better vehicle and better value ultimately depends on what you want to do with the truck.
Wait for the experts to chime in, but I think the Isuzu 3.2's have the same #1 cylinder oil starvation/disapearing oil problem that the 3.5's have. Make sure she checked her oil regularly. If not you may need to budget for a new engine, it may however last forever too. A remanufactured long block, either 3.2 or 3.5 is about $4,000 after the dust settles. [EDIT: That sounds really wrong, make sure the previous owner checked the engine oil regularly.]
Compared with the Toyota, hmm, good question. Well, neither of them have any power on the highway, but enough grunt for slow off road travel. The Toyota is bigger, you can decide whether that is good or bad. The Trooper should get better gas mileage, but not by tons and neither will be stellar. The Trooper has a much nicer interior than the Fj60 and perhaps a little nicer than the FJ62, but the Toyota's spartan interior is screwed together much better than the Isuzu's nicer one. The Toyota has a much larger selection of mods and goodies available (including new Chevrolet Vortex engines if you are so inclined), but if all you want are basic improvements (bumpers, suspension, lockers, axle and transer case gears) you can get what you need on the Trooper. The Trooper has ambulance style cargo doors where the Toyota is clam shell; which provides a table surface and some minimal protection from the rain, but also gives you struts that you have to replace periodically. I imagine you will be able to sell the Toyota for more than the Trooper when you are ready for a new ride. The Trooper is a more comfortable highway and mall car where the Toyota is more utilitarian truck.
For me it comes down to this. If you want a comfortable car to drive around town and take on some trips, buy the Isuzu. If you are looking for the ultimate expedition platform and have visions of modifications, or simply need more room, it is hard to beat a Land Cruiser. Please don't take this as my bashing the Trooper, I recently bought a '99. I had a tight budget and it fit my family's needs well. I have had a soft spot for the FJ62's ever since high school. My next door neighbor had one. It was bone stock and went everywhere (it was his dad's fishing mobile). Totally bullet proof and big enough to swallow tons of gear and people. They are very utilitarian and that appeals to me. The down side of them is that while there are good deals to be found, generally the ones in good shape command quite a premium. The other issue for me is size. While I long for cargo space, I am not a good enough driver to feel comfortable with a large vehicle on a tight shelf road when I have to pass someone.
If you want to discuss value, I think you can buy a better truck for less money with the Trooper, but I think you can build a better vehicle (that will be worth far more down the line) starting with the Toyota. If I spent less time on the highway and had more money to spend (and if the Trooper didn't fall in my lap) I would have bought a FJ62 and planned a rebuild.