in fact it is a real sequel, but with a complete different story
You contradicted yourself there, buddy. If it's a sequel, it's a continuation of the storyline. Gameplay be damned, if the game does not carry on the story it's a spin-off or pseudo-sequel.
The SFC version has better level design, way better music (Konami pulled out all the stops, even including the signature Konami sample set), and some of the best graphics to grace the SNES.
To it's credit, the Genesis game isn't BAD by any means, and it has slightly better bosses, but honestly you'd get much more enjoyment out of the SNES version.