Crisis Core centers around Zack and the events with him leading up to Sephiroth's turning (I'm not sure if it goes up to his death or not). I think in it though he is, at some point, given a mission to track down a "rogue SOLDIER" who is (SPOILER)reported to be Genesis.

I think the secret ending means Square has an idea that they are thinking about. If they can't put it into a usable form, well they technically never said there would be a sequel. If they can put it into a usable form, well there was the secret ending to foreshadow its coming, so it isn't completely out of nowhere.