The Raspberry Pi has 4 USB 2.0 ports. It features USB 2.0 ports instead of 3.0 to keep the cost down. In this application that will not effect usage at all. Having multiple USB ports allows the use of Wireless mice, USB flash drives, external hard drives and a multitude of other devices. It also allows direct connection the Megasquirt ECM. This is by far the best connectivity option when interfacing between the two.
You can also use a USB to Serial adapter when working with older Megasquirt units without the USB interface. The device I linked to is the preferred adapter proven to work with the Megasquirt hardware. Some of the adapters found elsewhere have issues connecting or are slow to transfer data.
Another option for connectivity is once again the built in Bluetooth 4.1 Classic, Bluetooth Low Energy options. This makes using newer wireless keyboards and mice a breeze. No need to tie up a USB port with a wireless dongle. This option can also be used to connect to the Megasquirt ECM using a Serial to USB adapter plugged into the Megasquirt unit.
Additional inputs are available via the countless add-ons available for the pi. Devices such as GPS, Accelerometers, Analog to Digital converters allowing custom sensor monitoring and datalogging (custom coding required). The possibilities are endless.