Supposedly the Saturn can do transparencies and translucencies just fine... on 2D objects. on 3D objects, special software would have to be coded by the developer group in order to do so, as it wasn't really a native Saturn feature.
The problem is, since NitM is a port of SotN, a game that, though is plays in 2D, is actually using a 3D-friendly engine (pretty much everything is a texture on a polygon instead of layers of tiles), anything that is 3D that is ported to the Saturn that didn't implement its own code for 3D transparencies/translucencies would suffer. And since everything is basically 3D...
This is basically a case of shoddy porting, rather than an inferior system.
The Saturn did a better job with the music and the looping, as I've mentioned before, so in that regard the Saturn does a better job, using PCM instead of XA audio, which means higher quality music that would loop more seamlessly.