As long as the characters, artwork, and music is different enough, and they aren't using any of the original code, level design, or other IP... then they aren't infringing.

The difference with most fan games is that they are using the original games characters, artwork, music, etc...Even if they are using original creations of the IP and not just ripping it out of the old games then it would be still copyright infringement. I guess the question here would be if the level design was in fact a carbon copy. But even then, Sega isn't Nintendo. They have traditionally but much more supportive of such things.

And I would consider this more of a tribute than a clone. I know those aren't legal terms, but more to show intent. A clone would be nothing but a cash grab, while a tribute would be pay homage to the original. Being similar, but different enough.