Regardless of the development status of the platform, with serial interface it is entirely normal to design an application-level communications protocol. Application requirements vary so widely that there aren't really any standards, at least as far as I know. As I suggested above, use half-duplex if possible: it makes things considerably simpler.
For what it's worth as a platform MicroPython on the Pyboard is rock-solid including its serial and USB interfaces.
USB virtual com RTS/CTS?
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Re: USB virtual com RTS/CTS?
Peter Hinch
Index to my micropython libraries.
Index to my micropython libraries.