Ford's new motor hasn't been out long enough for me to say I would want one of those and it is the only one I would consider from them. I liked my LB7/5 speed Ally until it started eating injectors like candy, if it hadn't done that I would still have it (injectors = $$$). I currently like my 07 cummins, lots of power,easier to work on, I like driving a manual and to me it feels like a truck when driving(solid front axle).
Doing all my own work on the vehicle I would go with the 5.9 Dodge cummins manual. Less moving parts, almost no emissions (only cat and high pressure common rail in the final years), the front of the motor doesn't need removed to change the water pump, cab doesn't need removed to work on the top end (Ford actually brags that the 11's aren't that way, why was it ever?), injectors are easier to get to (Ford and LB7 for sure), cp3 is easier to get to, fuel filter is easier to change, 05 and on 5.9 now has EFI live, most of the known bugs are fixable (killer dowel pin, lift pumps...) the major one not is the poor blocks in the eary 00's, but they are avoidable.
Not doing all my own work I would be in a LMM/Allison. Last motor before all this urea injection, gobs of power, 6 speed Ally. This one mostly for the Ally.
As for the 11's on, the Dodge 6.7 seems to have less emission problems now than with the early blue tec motors. Still not running urea, but once they start it is right under the cab outside the frame rail behind the front tire. Not a good spot for off the beaten path and with a system that will limp the truck when ran empty. Last of the diesels to come with a manual, but the new HO will only have an automatic.
Chevy/Gmc same thing with their urea tank just on the oppisite side. Only automatic as well.
Ford is the only one whose urea tank is tucked up under the vehicle no more susceptible than the fuel tank. Also only comes in automatic.
All the newer automatics seem to be built well from stock if you don't start adding power.
If you start pumping up the power and have a need for speed I believe the Dodge 48re is getting very bullet proof. It has even found its way behind the duramax at the drag strip, but they have been being built for years replacing everything that breaks a piece at a time with a stronger better billet piece.