Macbook Pro 13 retina late 2012 USB2.0 or 3.0?

The built-in keyboard and trackpad are using USB2 on an internal connection since they have no need of USB3 speeds to operate. That is not your external USB ports. If you connect a USB3 drive to your USB port you should see an entry in System Profiler which will show your external drive and its USB3 connection.

Hard drives are extremely slow (anywhere from 50MB/s to 120MB/s). Just because it uses a USB3 controller doesn't mean the drive is capable of fast speeds. An external SSD would give you better performance. Even a SATA based SSD would give you up to 500MB/s transfers. Plus if your laptop is using an internal hard drive you will be limited by its speed as well.