I'm going to find out how the two compare... or try to at least... I know a guy down here with an 04.5+ truck with a Smarty, TST, EZ stack that's doing like 575rwhp on stock injectors... obviously you have to have the air and the drivetrain to hold it, but the costs on those are pretty similar between the generations.
the things I like about the 3rd gen so far vs. the 12v is: you can make some pretty decent power without changing the injectors... saves you a good $800-1000 (sorry, but I can't do the 370's, new eras, etc. once you run a higher end injector, you don't want to go back) You don't have to o-ring the head... My plan is to just drop a set of ARP studs in it as a preventative measure.
a head gasket job w/ o-ring/etc. is an easy way to spend $500 or so. if you're paying someone else to do it, the price goes up from there easily. whereas dropping studs in is pretty simple.
I REALLY like how uncluttered it is under the hood, and I can't believe how leak-free this truck is vs. all of my 12v's that had fewer miles on them.
obviously having to pay for electronics is a pain, but I think the cost is offset to a nice extent in money/time/hassle saved on some of the stuff you just gotta do to a 12v. And, don't get me wrong, I'm a 12v guy till I die. When a friend or family member talks about getting a truck, I try to push them towards a p-pump truck. BUT... at a given power level, the 3rd gen will be a much more drivable truck... broader powerband, less smoke, etc. I've never denied that. But the higher cost and lesser reliability than the 12v pushed it behind the 12v for me.
I still use my 12v to make my living. this is my toy