In a C&C you can still get the 6.8 V10, that's the way I'd go. But either way, I think both are great engines. I went from a 6.8 to the 6.2 and I love the 6.2 so far, it's a beast. I haven't towed with it yet, but I'm looking forward to it.
You can check on the Super Duty forum as a number of folks there have C&C's.
Not sure if you can get a C&C in a 250 or 350. Thought I saw somewhere it has to be a F450, which means you can not get the 6.2 you would have to get the V10. That's what we got at work for our bucket trucks. I may be wrong though with the configuration.
I currently drive an 92 F250 diesel, original owner. The current diesel offerings scare me off too with all the emission crap and the need to regen. I'm thinking a F350 dually but wondering on how much of a mileage hit I'd be taking with DRW vs SRW. I'd prefer DRW cause I'd be carrying 3000 lbs in the bed in the form of a 950 Jayco cab over!