Regarding the exhaust brake, I don't believe this option was ever offered with a 5. 9. Integrated EB's first became available with the 07. 5 6. 7.
I do recall Dodge offering an aftermarket EB as a dealer installed accessory, but it was nothing like the VGT-based EB that the 6. 7 offers on all engines. Someone correct me if I'm wrong, please.
If it were me, I'd go with the 5. 9. It is a study in simple elegance. It's a much simpler motor, lots fewer problems, and probably a better choice for lots of short trips since you don't have to worry about plugging up the DPF if you do lots of short trips and it never gets a chance to regen. I have a 6. 7, love it, never had problems with it but worry about the sheer complexity and long-term durability of the emissions crap the EPA has hung on this fine motor. More parts=more things to go wrong.