So rather than toy around with my Supergrafx any more I just decided it'd be easier to emulate GnG for the time being. Finished it twice through and I think its a awesome port, I can see why its often held as the best of the console ports. Only two issues I really have with it - the first is the cost of the game + console. The port is good, but the improvements over the MD version feel minor at best, it has extra bits of animation here and there and it manages to push a few more enemies on screen to make it feel closer to the arcade version (not without sprite flicker on the final level though, which is ultra annoying) but its really not worth the console (or hassle!) in getting a Supergrafx just to experience a slightly better version of the game.
Second is limited continues. There is a cheat to push that up to at least 9 but still there are a couple of choke points in the game (3-2, 4-2 and 5-2) that still cause me a few problems, so having a limit only makes things more tense.
So I'd probably still side with the MD version of GnG being my preferred port. It runs super fast, is only missing a few graphical tricks here and there, has infinite continues, it has better music (in my opinion) and for some reason I just prefer the Arthur sprite from the Mega Drive version (no idea why). But really, Supergrafx or Mega Drive, you can't go wrong. And GnG is still probably my favourite of the series, perfect length, great level design and an excellent soundtrack. Only issue I have with the game in general is the boss of level 5 seems impossible if your not careful since his swarm attack seems impossible to dodge if he gets you in a corner, and Loki is the biggest pussy in the entire game (its the biggest anti climax to playing the game through two full times).