1. As other saids, torque management is the major reason for the truck feeling held back in first and second. All the current diesels do not give you 100% power in the lower gears and if they did then you would not able able to hook up off the line. You would also be replacing tires and transmissions every year if you completely took it out. While the Cummins with torque management still gives you more torque and power than the gasoline equivalent at the same rpm, it still feels held back. Once you hit third then you are getting 100% which is why it feels like the truck just pulls you when you hit third.
2. You have to know how to drive a Cummins(or any diesel). It is not like a high revving V8 that you just floor it and go. You have to roll into the throttle gradually ramping it up utilizing the strength of the diesel which is its massive amount of low end torque.. If you are going about 40 on the access road and floor it get on the highway on-ramp, then the truck will drop down to second gear where you are not getting full power(torque management) and you will be going nowhere fast. Not only that, but due to the low max engine speed of only 3,000 rpm in the Cummins, you will not be in second gear that long wasting even more time shifting to third. If you learn how to roll into the pedal to accelerate while remaining in third then you will be hitting 75 mph before you know it. Trust me, the Cummins has enough torque to pull you quickly onto the highway in third gear. You just got to learn how to utilize all that low rpm torque and how to make the truck accelerate without downshifting.
Same goes for when you want to accelerate at highway speeds. If you want to go from 65 mph to 75 mph, you don't floor it . With a Cummins, you just barely roll into the pedal keeping it in 6th or 5th and the torque will pull you to 75 mph quicker than flooring it would. Spend a few weeks behind the wheel of one and you will know what I am talking about.
3. As BossHogg said, you don't have to delete any emissions equipment to get the power or better fuel economy with the current engines with SCR. You can add a lot of power that you can feel while keeping the emissions equipment on. Just prepare to beef up the transmission to accommodate for the newly found power.