On Power Commanders site, they have different PCIIIUSB part numbers for the SP1 and SP2 unit.
From the feedback I've received from Power Commander, either will work fine.
The older PCIIIr has the ability to adjust ignition timing, but that feature is mostly useless you are a professional racer with the facilities to properly adjust it.
Otherwise you can potentially destroy your engine by improperly tweaking ignition timing.
Still the PCIIIr is a very capable unit.
The PCIIIUSB also samples fuel mix data at twice the rate as PCIIIr.
The PCIIIUSB model is now a modular unit and you can add on capabilities later, such as ignition timing, quick shifter, etc.