Hmm... thou hast a good point. Well... as long as I'm changing things (lol) I may as well think up some way to fix that problem. SPOILER: the only thing that was said in FF7 was that Jenova was another race, came from the sky and that she was superior to the ancients, right? Suppose KluYa, as a lunarian scientist, decided to try and genetically engineer a few humans to be on the same level as lunarians, to speed up the process of getting to the blue planet... producing Zemus and Jenova. Then when they went bad, the lunarians used the crystals to cast stop or hold, maybe, on the entire moon as a last ditch effort, and only Kluya, his half human sons, Golbez and Cecil, escaped, on the big whale maybe. FuSoYa(being the caster) was immune, but stayed to hold the power of the spell if it ever failed. Zemus was then physically parylized, but had developed mental powers to the point where he could do all the stuff he did without being able to move. He caused a malfunction in the big whale, which crashed into the ocean. Golbez and Cecil survived, but KluYa died. Then at the end, Jenova escapes the moon before the Lunarians take off into space in an escape pod.
There. That makes a bit more sense.