As you can see from the pics below the controller has the convenience of having a battery port, ample room inside of it as it's about 1.5-2 times wider than a standard 6-Button pad and already having a switch that can be used as one for on/off making it a seamless mod.
Also the receiver has ample room inside of it as well making for plenty of space for an RF receiver inside of it hopefully without any complications.
Anyhow all I'd like to do is find some way to make these guys work on RF tech and slap an old school dull red LED into the IR transmitter/'viewing window' at the top of the controller to both tell when it's on and match the Genesis' style.
Here's a link to a similar mod, except it used Genesis/SNES/NES controllers and adapted them for RF on the Wii as impromptu Gamecube/Classic controllers in case it would help:
http://www.ppl-pilot.com/
Here are some pics:

