Can you turn off usb protocol and use the USB port as a regular serial port?
You will need a cable to connect the MCU up to the computer no matter what you do. If you were using USB transport end to end then obviously that would be a USB cable. 

Since it appears that you want to use the UART out of the MCU to communicate and you do not want to put a UART to USB bridge IC on your circuit board then the solution you need is simply a different style of cable with the bridge chip built into the cable end. One that would do nicely is the TTL232R-3V3.

 

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