Nah, IR controlers are crap. Too sluggish at times for my liking. Fitting the Mega Drive control ports in to the Saturn's slots will be easy with a little bit of design work and a very sharp cutting tool. Yakumo
The X'Eye next to me has wired controller ports. If you were extra cool you could wire them up to a set of Saturn controller ports (being I heard the saturn was compatible with genny controllers why not the opposite?) and have it fit the case just fine. Or maybe an adapter for genny->saturn.