It doesn't matter if Genesis wasn't in the original game, he still started what Sephiroth would later become. And think about it, Crisis Core was released for YEARS after the original game. Because the writers of the compiliation are stupid, the story is all over the place. Heck, there's many different interpretations of that battle between Cloud and Sephiroth in the Nibelheim reactor ...but genesis wasn't in ff7 at all. they don't even mention him. i think when they made cc they just added genesis as another character so the game could have a main villian other than sephiroth. so yeah, in the original, genesis has nothing to do with sephiroth...
But ontopic, no. He's not the best villain. As others have stated, there have been far more successful villains. Kuja, Kefka and even Sin to name, but a few. Kuja destroyed Terra and even would use Ultima to cripple the party at the end of a fight. Sin could wipe out towns and cities without breaking a sweat.
Sephiroth may keep coming back, but he'll never ever accomplish his goals whatever they are or how twisted they are.