It's probably better than what the original poster has made, however you can debug with gdb directly on the hardware with the simple design of bidirectional com

It's probably better than what the original poster has made, however you can debug with gdb directly on the hardware with the simple design of bidirectional communication / dual port RAM and a little bit of ROM code to boot your debug code into the Genesis / MD memory. That's what we did. Single stepping is supported by using 68K trap instructions. The command set isn't very big. Mostly read memory / write memory / Run. I can't remember how we implemented stop but IIRC it was polling from an interrupt routine that was running from a timer. In any case you can get a lot of mileage out of a simple bit of hardware.