This is just a potential theory that doesn't contain spoilers per se. What if Sephiroth/Jenova is trying to destroy the other worlds in an attempt to bring forth Omega? And the reason they are so hellbent on controlling Cloud is to have him act as a Trojan Horse to the Lifestream?

He's the only one that has acclimated to both Jenova and Sephiroth cells. But as a natural born human, he has the capacity to be broken down and enter the Lifestream. If they use him to mass taint the stream while Omega is gathering it, it will cleanse the planet of humanity and end rebirth.