2006 to 2008 saw a big change in engines. Ford went from the 6.0 to the 6.4 and GM went from the 6.6 LLY to LBZ to LMM. Most of them saw a 50 hp and 100 ft lb increase during this time period.
You mentioned easier towing over hills. What did like better in the two year old newer truck over the older one? Was it the additional power of newer generation engine, the softer ride of the GM, interior comfort? You mentioned using a different hitch on the newer setup which also can change dynamics...
I'm curious since my 6.0 did well bumper towing 11,000+ lbs with 1000 lbs in the bed over the Continental Divide and still performs well with 4000 lbs in the bed while bumper towing 7000+ lbs. I never had the desire to upgrade the stock power so am surprised you were disappointed in performance.