I have a bone-stock 2001 Sport (6cyl., auto, NP232) that I bought in February with 81,000 on the clock. After putting 17,000 miles on it since then, absolutely nothing has gone wrong with it that I didn't cause myself.
The one major issue was killing the TPS through a combination of spray-washing the engine and hitting a deep water crossing hard. Having said that, this is a common XJ affliction and not unique to this year or the later models. It was also my fault for soaking it, so I got what I deserved on that one.
Power delivery is noticeably improved over earlier models with the torque peaking 1000RPM lower. Interior noise is considerably reduced, too. The coil rail that replaced the distributor and ignition wires is a major improvement in terms of ignition system water-resistance, IMHO.
All the electrical toys (mirrors & windows, in my case) work fine despite having been subjected to a fair amount of mud, dust, water, and snow. I love the ABS.
The suspension has needed to be replaced for the last 10,000 miles or so. The stock setup just doesn't seem to be very long-lived off-road; a couple of people I've talked to with similar vehicles have said the same thing. Then again, if you're planning on lifting it anyway this probably isn't much of a concern. Overall, off-road ability does not appear to be any better or worse than any earlier model.
People will tell you to avoid the run-out models - why, I don't know. The LP 30 is a consideration, but if you're going to run lockers or similar it makes sense to swap out and regear anyway, probably with a D44, so it's a moot point.
One other thing: the 2000 and 2001 models are statistically likely to have the lowest mileage and lowest instances of abuse since most are going to be coming back from one-owner leases at this point. In theory, this should give you longer-term enjoyment of the XJ with less downtime.
I'd say go for it, but then I'm biased