I prefer manuals. IMO the 5-speed would be the better choice for the daily driver, and the 6-speed for the haulers. Its been reported that the 12-valve engines get better fuel mileage than the 24-valve engines. However many people have gotten the 24-valve well into the 20MPG territory on the highway. The 94-98.5 12-valve trucks have a solid reliable P7100 injection pump that will go strong for hundreds of thousands of miles. A VP44 will go for sometime with a quality aftermarket lift pump system and a lubricant additive such as 2-cycle oil. The 24-valve also doesnt require the periodic valve adjustments that the 12-valve did. In fact Cummins recommends setting the valves on a 24-valve at 150,000 miles.
If it were up to me I would go 24-valve. Electronic tuners are great for on the fly adjustments, and the powerband seems broader when towing and daily driving. The lift pump systems and VP44 can be taken care of if you keep it lubricated and supplied with fuel. That isn't to say the 12-valve isn't capable I just prefer the feel of the 24-valve.