Hi MarkVS,
I own a 2004 NP Pajero Exceed 3.2 diesel. I brought it secondhand with 47,000km, and it now has 162,000km on the clock.
At the time I purchased mine, I narrowed my choice down to the Prado and Pajero. Both are good vehicles, but there were a few reasons that I ended up with the Pajero (which may not be applicable to you now).
Firstly was value for money. My Pajero being an Exceed it is top of the line. It has lots of luxury features as well as lots of electronic driving aids making it a very comfortable rig for a family tourer. For the money I paid for my Pajero, the best or nearest equivalent Prado I could find at the time was a TX (lower spec than a Grande), which was not as well appointed as the Pajero Exceed, had 95,000km on the clock (double) and was still $10k more. Put simply, I could just get "more" car, for less money, buying the Pajero.
The next deciding factor was the engine and driveline. The 3.2 DiD of the Pajero just eats the 3.0L of the Prado (of that vintage) in everyway. The Prado diesel isn't a bad engine (I owned a KZN-185 Surf previously that had one in it), but when compared with the Pajero, it's simply a slug. On paper the difference is obvious - Prado 96kw with 343nm, Pajero 121kw with 373nm. The Pajero also came standard with a 5 speed triptronic autobox, versus the Prados 4 speed box, which makes very good use of the low down torque of the 3.2 engine.
The next thing which won me over was the Pajeros handling. It just felt so nice to drive, feeling more car like on the road and sporty compared to the Prado, which felt slow, heavy and un-responsive and more like a traditional old school 4wd. I'm guessing the major difference here being the Pajeros independent suspension and monocoque chassis.
Next and probably final major thing was the Pajeros warranty. When I brought my Pajero it was a little over 2 years old, but still had almost 3 years factory warranty. I know this wouldn't apply to your situation, but I think the 5/10 warranty offered on these cars from new was and possibly still is the best on the market, which I would suggest reflects the confidence Mitsubishi has in these vehicles.
There's other things which I thought were better in the Pajero over the Prado (like the way the 7 seats fold away under the floor), but I think these are probably a more to do with personal opinion.
So after owning my car now for 5 odd years and 110,000km, I'm still really happy with my choice. Apart from the usual servicing and parts that would typically be replaced (brake pads, air filters etc), oil changes at 15,000km instead of 5,000km for the Toyota, the only thing which I've had to replace was the starter motor, which started playing up just recently after 160,000km - which is not a bad length of service. The car is my daily driver, my weekend tow vehicle for my 21 foot boat, but also gets used 2 -3 times a year for family 4wding holidays and has been ultra reliable, fuel efficient and comfortable.
As others have pointed out, the direct injected diesel of the Pajero is noisy at idle and during acceleration, but quiet at cruising speed. In all honesty the diesel "chatter" doesn't bother me, and it's hard to hear the noise over the AT tyres, modified exhaust, 2 young boys in the back seat, and the wife chewing my ear off in the front seat.
Hope this ramble helped. Good luck, you won't go wrong buying either a Prado or a Pajero in my opinion anyway.