I've only owned the 2006 Mounty, so can't give comparison. But you should note that the torque output did not change by much (may be identical, can't remember) at around 300ft-lbs. Same torque, but increased hp, (and all else remaining the same!) usually means you don't see the benefits off the line, instead seeing the engine with an ability to spin faster and/or breath better at higher rpm.
That said, all things did not stay the same. 2006 V8's got the new 6 speed as standard equipment, including a much lower 1st gear (compared to the 3rd gen 5-speed), with no need/option for 3.73 axle ratios. So here is what I would expect, which you will need to confirm from others who have tried both:
4th gen V8 (6-speed, 3.55 axles), compared to:
a. 3rd gen V8, 5-speed, 3.55 axles (std class II towing): 4th gen better off the line due to lower 1st gear, better towing ability due to lower 1st gear, lower cruise rpm due to double-OD, stronger top end due to increased hp (at higher rpm)
b. 3rd gen V8, 5-speed, 3.73 axles (HD Class III/IV tow package): 4th gen probably about the same off the line, and same towing "feel" since 1st gear final drive ratio will be similar. Much lower cruise rpm and increased fuel economy due to double-OD and friendly 3.55 axles. Increased high-rpm power (4th gen) may not be felt in comparison, becuase of the different axle ratios.
In short, I would expect no downside to the 4th gen powertrain, but improvements in feel or fuel economy, depending on whether your 3rd gen had the factory tow package or not.
