Bah, I know I'm two years late, but meh.
The issue with this, however, could probably be that Sega is now a third-party developer, yet Nintendo is still in business as a console developer. Nintendo may be less willing to allow the SNES version of the game be placed on a competitor's system... so they went with the Genesis version, seeing as how Sega releases games for all major consoles. This might be me being dumb at 1:30, though, so I really don't know.
I'm also weirdly disturbed at how disliked NHL95 is... though that's not exactly the topic here.