The 5.9 is basically a bored and stroked 5.9 so in that regard it's pretty much bulletproof. The only gripes I hear are about the DPF and EGR systems which have really hurt fuel mileage. We just have to hope that the engineers can come up with better solutions to the emissions problem than those two.
Check these forums out. If there are any other gripes they'll be covered here;
I see 20-22mpg non-towing hwy mileage with my 2006 5.9. There's almost no hope a 6.7 will ever match those numbers. If I had a 6.7 I would put a vegetable oil fuel system on it to reduce fuel costs. There is a Golden Fuel Systems installer in Houston. Give Bud a call and discuss it;