5.9Ls exterior wise have the hood vents, rocker panel skirts, the grille, low profile roof rack, and the 16" ultrastar wheels over a standard ZJ. The interior has more leather, a charcoal head liner and a rear sound bar over the standard ZJ. If you are looking at a 5.2L vs the 5.9L get the 5.9L. The 5.2l Isn't that much of an upgrade from a 4.0l. The only upside to the 5.2L is that it has a marginally better transmission than the 42RE. My 93 ZJ w/ 4.0L got better mileage than the '97 ZJ 5.2l I have now. The 93 got 20-21 on the highway and the 5.2L gets around 18. The only reason I got the 5.2L vs. looking for another 4.0L ZJ is because the price was right. The 5.2L does sound nice with a decent exhaust though.
As far as comfort I find the seats in my 00 XJ limited much better than the ones in the 97 ZJ. The ZJ seats have non existent lateral support. The ZJ does have auto lights, auto climate, etc. It might be slightly quieter than the XJ. The ZJ does have more room than the XJ.
Personally I would look into a WJ with the 4.7L HO if you want more storage. Having the spare tire under helps a lot with room. The Wj 4.7L gets about the same mileage as a 5.2L ZJ. A lot of work was done on the WJ to make it quieter and more comfortable than the ZJ.