The modern six speed automatics are vastly improved over the old 47RE/48RE automatics. The automatic transmission, exhaust brake function, and engine controls are skillfully and fully integrated. Try one, you'll like it.
Six speed G-56 manual transmission equipped trucks, unfortunately, are equipped with the lousy dual mass flywheel/clutch system for the purpose of reducing noise, vibration, and harshness (NVH). The design does accomplish this, these trucks won't rattle the transmission if you lug it down to parking lot speed in third gear then accelerate like my old '01 HO/Six speed NV-5600 truck did.
Many owners of G-56 trucks who tow heavy, tow a lot of miles, are have simply accumulated 60,000 miles or more are reporting clutch failures or even multiple failures. Many convert their trucks to conventional solid flywheels and clutches from South Bend Clutch or other vendors. The solid flywheel works fine according to reports but generates a bit of unwanted noise which some find objectionable.
Manual transmission equipped trucks and cab and chassis trucks like mine are limited to 610 ft. lbs. of torque, not the full 650 the engine is programmed to produce when the new MOPAR six speed automatic is selected.