What's wrong with the 5.4???
As far as the 6.0 is concerned, it is NOT difficult to diagnose or repair. The problem is few want to learn how. It really is simple. Same basic functions as the 7.3 with EGR and the VGT added. There is nothing complex or hard to fix about it at all. Too many blame driveability issues on programming, rather than fixing the truck.
The biggest lesson that most DON'T learn when learning to repair them is when there are repeat repairs of the same systems, there must be some other root cause. One truck I know had 13 injectors put in it by the same dealership. 13!!!! They just kept putting in injectors that were failing, not fixing the root cause, which was a HPOP having pups slowly puking metal into the injectors and killing them. Had the owner not changed dealerships, he would have just kept taking it back, and they wouldn't have fixed it, just fixed the symptom, furthering the 'they are all junk' B.S. that is so very rampant on boards like this.
Most of the problems arise from fuel issues including pump/pickup (45 psi minimum is CRITICAL), too long of oil chage intervals with wrong oil (remember oil fires the injectors), or customers using them as they weren't designed to. (tuners, lots of idling, etc)
As for fuel, The EPA gave the oil co's a waiver after the hurricanes down south for how much they have to refine the fuel, and it is very noticeable. Combine that with record fuel prices that have distributors feeding anything that will burn into the mix and the increased use of biodiesel, and you have fuel that is absolute sheet. Biodiesel will not actualy damage the engine, but it will damage the tanks and lines leading to fuel supply issues. (GM and Dodge are having troubles with this too) 5% biodiesel MAX!!!!!!!!! Moreover some aftermarkets sell the fuel filters seperately. The HFCM's primary filter is more important than the engine mounted secondary, yet because people see it as harder, they rarely change it.
Some complain about the lack of throttle response on the low end. You can thank the EPA for that. Since California declared particulate a carcinogen (sp?) the EPA has cracked down on that and all other diesel tailpipe emissions, leading to less fuel injected out of the hole because there is less boost available at idle. Less boost is less air. Less air must have less fuel injected to not cause higher emissions.
To say that the other makers don't have troubles is hooey too. They have issues too due to the fuel and emissions standards.