I owned a 2004 SRW 3500 SLT with a 5.9 for 6 years, and I traded it for my current 2014 2500 Mega cab Laramie (black, sport) with a 6.7. I bought it new. The 2004 was better off road due to the shorter wheelbase and bigger lift (the 14 is over 18" longer than the 04), but I do like the mega cab for hauling passengers and inside cargo. There is no question that the coil rear end on my current 2500 gives a smoother ride than the leaf springs in the 2004. I have had no significant trouble with either truck. Both trucks had/have 35's. The 04 was leveled. The 14 has stock suspension. No tire rub with either truck. The 04 was over 7' tall as I had it configured. My 2014 is about 6'10", so some parking garages are a problem.
The 5.9 is more simple -- no DEF/SCR/DPF; only one fuel filter. It had a manual transfer case as well. The 2004's had cats, and my truck was not deleted. The truck was very reliable. I replaced a water pump, AC compressor and front diff seal. It needed new batteries every 2 years without fail, but that is not uncommon in PHX.
The newer truck has a much nicer interior and much better NVH. It is great on long trips with decent economy. The 6.7 has had several recalls (I believe that newer trucks were better sorted), and I recently replaced the touch screen radio (bricked during an update, BUT I was able to wrangle a goodwill warranty replacement) -- radio and climate controls are in the unit. Batteries have been changed, and I had a coolant fitting replaced to fix a leak.
I am torn. I really liked the simplicity of the older truck, but there is no denying the comfort of the newer models. With respect to power, the 5.9 was very adequate, even with a 30' loaded toy hauler. The 6.7 is better, certainly, and the integrated exhaust brake and brake controller on the newer truck are nice.
I think there is a reason that 5.9 trucks in good condition command a premium. I do not deny the attraction. Parts are plentiful, and the major components of the truck are quite reliable. The lack of DEF/DPF is a plus. I would have no problem going back, but I do like the 6.7 (particularly the creature comforts -- heated/ventilated seats, etc). The SCR/DEF/DPF system on my truck has been good, although there are those who have had problems. That is my biggest source of concern in the long term.
I really like diesel trucks, and, although the cost of entry is higher, resale is generally much higher as well, so I see that as a wash. I enjoy the range. If I am conservative, I can get well over 500 miles with onboard fuel (that was true with my old truck as well). My wife is much happier in the new truck, but she had no problem driving the old truck either. It was just louder and a bit rougher on the road when unloaded.
I think either will serve you well.