the apps are mainly dependent on ram,cpu,&gpu.. raid setups, hard drives, pci cards etc-- that stuff doesn't really matter for app performance (at least the applications i'm familiar with)..
i'm pretty sure the new mac will out perform the current one when it comes to running software
the battle or whatever would have to be less application based (even though that's the main importance imo) and more about storage/data moving workflow.. (though again, i don't really see how the new mac would lose this battle either.. it will lose when cost comes into the picture because it's going to cost additional money for the external enclosures needed with the new mac)
Agreed.
But a simple comparison would be simply to try and equip a 5,1 Mac Pro with the same gear as the new Mac Pro... Dual W9000 FirePro GPUs, USB 3, and a PCIe SSD that tops 1.2GB/s... (The sad truth is that this is impossible thanks to the slot arrangement in the 5,1. And affordable? I doubt it).