There is no absolute, yes/no answer when it comes to whether to buy a 6.0, IMO. It depends on several factors. It came in the nicest PU trucks they ever made, (I like them better than the new ones), and they are awesome engine/trans combos if left stock and maintained by the book. It's important to mention that scheduled maintenance on modern diesels is crucial. They are not as forgiving as gas engines when an owner skips oil or filter changes. (Air/fuel/oil). I bought my 7.3 w/ a blown engine @ 157k miles because someone never changed the oil and a piston-squirter got clogged, frying a piston and breaking rings. It was not the engine's fault, that thing would have gone 300k easy w/ proper service.
The 6.0 is unique among modern TDIs in that it
really doesn't do well with chips/tuners, at least not w/ stock head bolts. One reason is that it's a very high specific-output engine in stock form, my '05 makes 570 lbs. of torque from 6 liters. It doesn't take Stephen Hawking to explain the physics of that. It also has 4 valves/cylinder and fewer head bolts than a 7.3. The 7.3 PSD can easily handle another 100 hp tuner if other intelligent mods are made, such as exhaust and gauges. (To monitor EGTs while towing, for instance).
Since I bought my 6.0, I've been obsessively reading and posting on this diesel BBS:
http://www.thedieselstop.com/forums/f23/ It's sort of like the Pelican 911 tech board with lots of pro diesel techs and lots of road mile experience on it. There is a definite pattern to the posts in that a large number of problems involve modded trucks or used trucks w/ unknown service histories. There are others than claim real lemon stories but w/o knowing all factors, it's hard to get the full story. BTW, lemon stories are present on all truck boards. (Ford/GM/Dodge).
My truck is bone stock and still under factory engine warranty, which is 5 yr./100k for all manufacturers for diesel PUs. I did not get records w/ it but all signs point to a reasonably well-maintained truck. When I got it, the CEL light was on but I did not care because of warranty. It turned out to be an EGR fault+turbo code, they replaced EGR and cleaned carbon from turbo free of charge. (6.0s have a variable vane turbo which can get coked-up making vanes stick). Both of these procedures would have been DIY possible for the mechanically inclined if out of warranty. This improved power and mileage. 2 weeks later, CEL was back on w/o any real driving or running symptoms. I brought it back to dealer, turned out to be a fuel injection control module putting out low voltage. Replaced under warranty, truck now runs like silk and fast as hell.
Before you scream, "what a POS!", I should mention that modules and sensors go out on 7.3s as well. Visit the 7.3 board at that site if you don't believe me. Neither of the services that I needed would have left me on the side of the road, just made the truck run less than 100%.
I absolutely love my truck now that it's sorted-out. I have all new factory filters and fluids in it and add a good lubricity additive to every tank which really makes it quiet and saves the injectors. (A good idea on any diesel that is not the very latest edition running ULSD). The new diesel fuel has terrible lubricity. If you can get even 5% bio-diesel in your area, that is the best lubricity additive out there. There is an excellent scientific study on this here:
http://www.thedieselstop.com/forums/f23/fuel-addative-lubricity-study-231198/
That all said, I'm a lot more comfortable w/ this engine if it's under Ford warranty and if I keep the truck I will probably extend it. Ford offers an additional 2 yrs./100k miles for about $2k. Even w/o a warranty, it would probably be fine if I maintain it religiously and keep it stock. It's a really nice truck, just amazingly smooth/quiet power. It just whistles down the road like a quiet jet engine. Can't wait for my road trip this week.