I've owned a Mk1 Shogun and a 120-series 3.0 D4D. I've also driven Mk2 (2.8 diesel) and Mk3 (3.2 diesel) shoguns. The latest landcruiser is the 150-series, which only came out in November.
The D4D engine had a reputation for blowing injector seals at 60,000 miles or so, but the later 120s (from 2008) and 150s have the upgraded (aluminium) seals as standard. I've heard of a few shoguns suffering (auto) gearbox failure at about the same mileage.
I think that the complexity of these engines to get them down to such low levels of CO2 have made them both potentially less reliable than the earlier cars (I think Toyota's peak was the 90 series [colorado] and 80 series [amazon], and I think mitsubishi's peak was the Mk2) - but all three models are now over 10 years old).
When I faced this dilemma a year or so ago, I chose the Toyota. Mainly because I thought the drive was more refined, partly for the residuals (Shoguns drop quicker) and partly because I had a good local toyota dealer.