Like you're probably getting by now, I'm probably not the best person to ask for opinions. I tend to weigh each vehicle against its merits. I've got NO brand loyalties. I'm not a fanboy, I can't afford to be in my trade / profession.
What is your definition of an off-roader? Something that can glide over the rough stuff at speed or go through tough axle-twisting speed at crawling speed? For most people, a Pajero will largely suffice. I feel it's more stable at higher speeds over rough terrain, which is what most people might encounter. Contrary to popular belief, the axle flex of a Pajero is almost on par with a Prado's - that is to say, the height one tyre can be raised before one of the other tyres leaves the ground. Although if you want to modify it, the LC is easier since it's got live axles all around.
The IFS gives better steering accuracy on the rough stuff as the unsprung weight is a lot less. As the two tyres are not connected, each tyre is free to act on its own, so the road holding on the rough stuff is much better. I've seen 100 series LCs having the inside front tyre leave the ground going over a light bump in a corner on-road. I haven't seen anything similar with a Prado, but since it has a live front axle, I believe it wouldn't be any better. You'll never see that in a Pajero.
As far as on-road ride quality is concerned, I feel that the Pajero manages to feel firm without shaking you about. It gives you excellent feedback. I haven't driven the new ones a lot, but the older ones give you a very clear picture of what's happening under the tyres.
Engine? People say they overheat and sieze. It's not the fault of the engine. Don't rev it to the moon everytime you change gear. Max torque is at 2000 RPM for most models. Keep it around that RPM maximum if you want good progress with good acceleration. The older MFI IDI (Mechanical Fuel Injected Indirect Diesel Injection) engines could rev to above 5K (I know from experience) and might spin fast enough to destroy themselves if you tweak the injection pump. The EFI ones have a relatively low-RPM torque curve, so you might have a tendency to change gears earlier, that and most are Auto.
As for Toyota engines, I'm not even sure if the Prado engines are any better. I've heard horror stories in both camps. What I can say is this, all diesel engines will suffer if you skimp on maintenance. Saying that such-and-such engine that takes more abuse than another one is a meaningless quality. You should know your cars limits. If you pass them, be prepared to pay the price. As far as siezing is concerned, there's a temperature guage on the centre of the instrument cluster, look at it from time to time, it's there to be seen. If it goes up, ease off. If it continually stays high, have your cooling system checked. Coolant, thermostat, water pump can be changed, purging can be done. It's a good cooling system. A cooling system that can keep the engine cool while keeping the A/C running at 50+°C indicated outside temperature in a traffic jam is good enough for me.
Other issues? Parts availability / price. I can't comment at all on these things. I know for a fact that even though the Pajero parts are relatively expensive, they last a lot longer as well, so the price per kilometer is not any worse than say, a Corolla for example.
Now for the big question, If I were buying a 4WD for the family having a good comfort and good features, I'd go for a Pajero in a heartbeat. It's a more refined vehicle overall I find. The engines are powerful. And as for looks, even though it's a subjective thing, I prefer the looks of the Pajero over the Prado.