WJ unibodies are a bit stronger and you'll get a bit more interior space. IMO, the ZJ rear suspension is a little better design, it's got more parts in common with other Jeeps and it's a little simpler in a lot of ways, being that it's closer to an over-grown XJ.
Personally, for an expedition rig, if you get a WJ, plan to take care of the 0331 head issue (or get a 4.7 that's been well maintained, they're not bad engines save for a few quirks but they don't tolerate being overheated at all). In a ZJ, get the V8. Other than the easily fixable plenum gasket issue, they're even more reliable / durable than a 96+ 4.0 (the point where 4.0s started getting not as good).
If you're planning to venture off into the wilderness, I'd tend to say get the ZJ (ideally a 96 - 98 with a V8). You'll have an easier time finding parts if you need them (front suspension and axles are compatible with the TJ and XJ, for example).
A 93 - 95 ZJ (4.0 or V8) or a 4.0 WJ (unless it has quadra-drive) will have a D35 in the rear. 96 - 98 V8 ZJs, all V8 WJs and quadra-drive 4.0 WJs have the D44a in the rear. The 44a could use a skid plate for off-roading, but it's a decently strong axle. All have low pinion D30s up front.
As far as transfer cases, get what you find. They're swappable if you want to later. All V8 ZJs come with the full-time case (NV249) anyway. It's a perfectly good case until you wear out the viscous coupler. And when the time comes, a 242 or 231 from a 96 - 98 4.0 ZJ or 96 - 01 XJ bolts right into a 96 - 98 V8 ZJ (the swap is a hair more complicated on 93 - 95 V8 ZJs).
Personally, I've got a 98 5.9 ZJ. I'd consider a WJ as a trail rig (and they do look good with big tires), but for an all-around rig, I wouldn't give up the ZJ for a WJ.