The biggest pi$$ off for me about my 6.0L was getting hosed so bad on resale, to the tune of $10-$15k less than a similar GM or Ram. Like I posted earlier, a lot of reputable dealers will not take them.
This is not bashing the 6.0L; it is fact and I can speak to it because I experienced it first hand. A cousin of my wife's had over $15k in engine warranty repairs in 60k miles on his 2006 6.0L and he finally traded it in a Ford 6.7L because it would still overheat when towing. Another good colleague and friend of mine had his 2005 6.0L die on him away from home; he ended up getting it towed the 250 miles home and had it bulletproofed to the tune of $8k. I thought my truck was pretty good in that it did not leave me stranded in 110k miles, however then it started to have issues that I knew were going to cost me so I made a move. These are far from isolated stories and anyone bringing them up in a constructive manner is not bashing. Remember Ford spent well over 1 billion dollars in warranty work on this engine; that does not equate to them being a success but rather a disaster. In fact I doubt there has been another engine in history with such high warranty costs, and I would bet that Ford would like to forget they ever marketed them because it has cost them a lot of loyal customers.
I am truly happy for anyone that loves their 6.0L; I loved mine in the day too. I really loved the Super Duty truck and just wished I had been smarter and shopped around longer at the time until I found one with a 7.3L because I would still have it. And just because you see a lot of 6.0L trucks around doesn't mean much; I would bet that a lot of them have had a boat load of cash spent on them to keep them on the road.