In some cases you want to avoid your programmers needing to know two designs, compiler toolchains etc - a microcontroller might push you towards using C, and perhaps all your other code is in Python and you'd prefer to keep everything in Python.

If you're making something like a high precision time server synchronized to GPS, you might want your GPIOs to trigger direct interrupts on the device with the ethernet port. Of course, IIRC the RPi has USB ethernet so it's not a good choice for a truly high precision time server.