I have a '92, sold the '99 with 178000+ on it, and bought a '05. I have almost 1200 miles on it. I traded from a regular cab to a QuadCab '05 because our family is growing and we hope it contiues to grow. The room of the '05 is adequate (read don't need a megacab, if they even happen) and a requirement.
It has about the same power (maybe a little more) as the '99 which I had a EZ on to get it there. I love the '05 so far.
Thoughts on the '05:
1) The in-tank pump may be a problem. It also may be the perfect solution to the 2nd gen lift pump issues. Time will tell. Not loosing any sleep over it.
2) Common rail injectors may be a problem, but aftermarket filtration should solve it. Filling up at trustworthy stations and regular filter changes / water trap draining on the truck are the best solutions. It may soon be possible to get a 2 or 3 micron drop-in filter to replace the stock filter. Time will tell. Not loosing any sleep over it.
3) Can't wait to tow with it. The 6 speed should be far superior for towing over the 5 speeds. Never had a problem with the NV4500, but there was a lot of space between the gears compared to the 6 speed. The 6 speed is built for towing, the 5 speed is built for racing / acceleration.
4) The family and I love the softer ride. The wife loves the quite

, but I think I will be solving her problem shortly with the opening up of the muffler and kitty.

The one thing that works in my favor on this is that our 5 month old daughter goes right to sleep with the roar of the straight piped second gen.

I love our little girl!

"Can you say 'Cummins'?"
I am not trying to talk anyone into trading to a 3rd gen. I got a really good offer on the '99 and a good price on the '05. Needed the quadcab for the family. It came together and it was time to trade. If none of the above had happened, I would still be happily driving my '99. It is still a great truck and yes, I had put a VP44 on it on my dime and two lift pumps. Everything has maintenance associated with it. What will the maintenance of the 3rd gens be? Time will tell.
The fact is that time will tell about the 3rd gens and the '05s. I am not loosing any sleep over it. This is my third CTD and there is not a bad one in the bunch!
Good luck with whatever you decide. There is no wrong choice, but everyone will have an opinion to the contrary.