If you no longer need to input or output multiple channels via your interface then it really doesn't matter what connection protocol you use.
However for maximum versatility I would always go for a "smart" connection like Thunderbolt or FireWire over a "dumb" one like USB.
USB3 has overcome most of the problems that the previous versions encountered simply because the bandwidth has been increased to a point where unless you need to pump lots of timing critical data through it, it no longer matters. However if you do use USB it is still a good idea to use the port that shares as few other devices as possible on the same bus. Remember that on a lot of computers it is not always obvious what else is on the same bus (built-in WiFi and bluetooth, keyboard, trackpad, webcam etc.) as each external USB port.