Well, we did it. We bought a new 08 3500 Dodge, automatic. We loved our cummins on our 2000, so we stuck with what we knew. I haven't found any bad reports on the 6.7 automatic. Since it has a new warranty, it was worth the chance we ended up with an awesome new truck! The power is awesome, the tranny was smooth. If only cummins and allison would marry!
I have an 08 Mega Cab with the 68RFE trans. So far I am thoroughly impressed with this trans. It is supposed to be Dodges answer to the Allison. The 6 speed auto coupled with the exhaust brake works absolutely flawless. Downshifts smooth and slows you down in a hurry, hardly need to touch the brakes. I don't know how they would hold up with extremely heavy loads, but if your doing medium duty towing as I am, I don't see any negatives thus far. I also am a member of several Cummins forums and I haven't really read anything bad about the trannys yet.
The 6.7 might be another story. I have had no trouble with mine, but I have read about a number of people having turbo issues due to the EGR sending soot back through the turbo.
Mileage is slightly less on mine than on a 5.9.
Hope that helps. Good Luck on your decision.