I'll take the TG16 version over the Genesis/MD version anyday, though I'm not saying it's light years better or anything.
Graphics - For the most part, the TG16 is the clear winner here, with a nice full screen, way more colors, much brighter, and even more detailed sprites. However some of the bonus screen, as a couple people here already mentioned, do look nicer in the Mega Drive version. However one of the bonus stages in the TG16 one was based off Dragon Spirit, so it sort of had to blend in with that game more, and the Mega Drive version kind of tore the style apart to make it look better, so I felt sorry for Dragon Spirit because of this. Overall, TG16 definitely.
Sound - I highly prefer the sound of the TG16 version. Everything sounds so much clearer and since I was never a fan of Techno Soft or Genesis' sound, the Genesis version suffered from that crunchy, rough sound I can't stand for the most part. The skull's evil laugh even sounds quite a bit better in the TG16 original.
Gameplay - Some may not even be able to notice, but there is a slightly different feel in the physics, and they tend to be a little worse in the Genesis verison. There's just something about how you are easily able to control your shots in the TG16 one, but the Genesis version suffers a bit and you just can't get that feel down. I'm not the only person who thinks this, so hopefully someone else can clean this up. However some of the new bonus stages in the Genesis one were really cool, like the one with that devil thing spitting fire. But once again, TG16 takes the cake.
So yeah, I prefer the TG16 original any day - it simply wins in all categories.