I think this would be very dependent on the application and the nature of the i/o, but with a microcontroller I think you would have a bigger freedom to program it in any way you like (e.g. C or assembly) and so could make speed improvements to your program if needed whereas a PLC would probably limited by the programming environment it uses.
But are you aware of our range of MIACs? These are ruggedised microcontrollers which should offer the best of both worlds, and we have a choice - PIC (8bit and 16bit), Arduino and Raspberry Pi. More details are here:
http://www.flowcode.co.uk/miac/
Regards,
Steve.