I own a diesel shop, I drive a Dodge. Long term ownership will be less with the Dodge for sure. Duramaxs are actually good engines, keep clean fuel flowing to them and they will go 500k no sweat. Same with the Dodge. To build a Dodge 48re "Correctly" to handle the torque of the cummins and last, expect to pay $6kish, installed. Expect to to replace injectors in the dodge at 150-175k. the 06-07 5.9s did have some issues with dropping valve seats, but there is no rhyme or reason as to when or if that will happen.
The Allison should last forever. Build quality is about the same between the two. Ride is way better on the Chevy. If you don't need 4wd, then the solid front axle shouldn't be a concern either, so the Chevy may be a better choice for you.
Hope that helps a little. There are some common issues listed on my website,
Left Coast Diesel Performance and Service if you want to check them out.