With the 3r you can adjust your ignition timing for a turbo, high compression, or nitrous engine. Thats it. Map tuning and ignition tuning all in one package.
The usb by itself will only do your FI. The best thing about the usb is it is modular and you can buy a switch that will allow 2 maps, a box that allows ignition timing changes, a electric shifter, and now offers a LCD screen you can mount to your handlebar or gauges that allows on the fly adjustments.
If you just want a map for a pipe I would think the 3r is good enough. If you will want to make more mods now or maybe in the future go with the usb.
My 2 cents.