The only thing I can say is ask yourself which truck do you like driving more. Also one thing I like about the 2nd gen is things seem to be more "modular". In other words, you dont have idle speed to set, or timing, you dont have a fueling plate to tinker with, just some things like that. W/ the 24v and a smarty, alot of things are tweakable with software. Also, basically, your VP44 is either good or its bad. You replace it and solve alot of problems without a bunch of tweaking involved. The APPS can be changed in 15 minutes. The downside is these parts are expensive and arguably can be unreliable. . Its all a judgement call. I just got a code saying the APPS voltage is too high, so I may be putting in a 4th one now. That is a problem for me. Im thinking the VP44's may be starting to be better than before with some upgraded boards, and tougher internal parts. They may not be so bad now, especially with the way everyone is upgrading the fuel supply to them. I kinda like my 24v now, and it sure pulls like hell I can say that for sure. The 12v may be a little more reliable ( just a guess from what ive read in the forums), but may require a little more tweaking when things come out of adjustment.
For me it would come down to which truck to I like driving better. Both can be made to run excellent.
Added: Just learn how to identify a #53 block and make sure you dont get one if you go to a 24v.