From my perspective the main advantages of the PCV over the PCIIIUSB are:
1) Small size
2) Optional Autotune feature
3) Can access the unit using power over USB connection (no external battery needed)
There may be other features, but these are my faves.
Othewise, I don't see the reason to change, unless the PCIIIUSB dies.
A word of caution. With any of the Power Commander units, be careful with those firmware or software updates.
I updated the firmware and software on mine and it induced a misfire.
It behave exactly how a bad coil, plug wire, or short would.
I worked with Power Commander to ratchet down several versions of firmware until I found one where the misfire stopped.
If it ain't broke, don't update it.
Also, as a side note. The Power Commander units don't come with a zero map when shipped.
They come with a map pre-installed for one's bike model and conditions Power Commander believes will work in your geographical area.
My PCV came with a map that was too lean in certain midrange areas that caused power loss and misfires at certain throttle settings.
After I installed zero map while troubleshooting my misfire condition, the bike now runs much better, and even sounds better.
I just need to fine tune the fuel mapping on a dyno or Autotune to finish the job.