I personally have owned a '96 dodge CTD, '99 dodge CTD, '04 GMC Duramax/Allison and now drive a '06 Dodge CTD.
I don't consider myself to be brand loyal. I have a Bachelor's degree in Vehicle Research and Design, and have worked as a professional Mechanic as well. Every manufacturer has their successful designs/products, and their failures out there as well.
I was very happy with the Dodge product. All of the above trucks were AT. The reason I left dodge and tried the GMC product, was the cab room. At my first opportunity, I went back to Dodge, and we now drive a mega cab.
I agree that up until recently, Dodge has been low-man on the tranny totem pole. But, that being said, they could be built to withstand just about anything you can throw at them as well. (yes, there are some folks that can break anything) for the same money as a new Duramax/Allison combo, you can go buy a dodge, and have a super-built aftermarket tranny and T/C put into it, and have a stronger package. Even the mighty Allison is not without it's issues, they have a weak spot in the output shaft housing, and tend to go out there.
While I am NOT brand loyal, I did have a negative experience with GM about my '04. I experienced that gauge cluster issue, and I was just over the 70K mile cutoff. I argued that you don't buy a $40K+ pickup do have to replace a non-serviceable, non-misuse-able part at 71K miles on my own dime. They didn't agree. Also, on that injector issue, while the warranty is good for 200K miles, they won't replace them as preventative maintenance, so when your crankcase fills with diesel, and your engine oil looses its lubricity as a result, they wont replace the injectors until after the damage is done (and they wouldn't agree to cover said damage). I didn't like that approach either. So I went back to Dodge. They had the Mega cab by then.
I have heard nothing but great things about that new 6.7 and 68RFE, but no personal experience. Ours is a 5.9 with the 48RFE, which incidentally, has a higher towing rating from the factory than the manual in '06. If you keep it stock, and don't tow more than 10K, you're probably just fine. If you want to tow more, and BOMB the truck, then start with the tranny, and then put a "SMARTY" controller in it.
When it came to towing, the GMC was in a different world than the Dodge. With my '99, I had to check my mirrors to make sure my trailer was still there. In the Duramax, (with the Edge Juice/Attitude installed) I kept thinking my trailer brakes were stuck on, or my bearings were seized. Very disappointing.
Based on my experience, my recommendation is go with the Dodge. And, today's auto trannys can be just fine, or built to withstand Armageddon if you want.
You can also check other Diesel-focused forums for great info. I recommend
www.nwbombers.com, and the turbodieselregister.com