Squall here is absolutely correct. As a writer, I am well aware of every permutation of everything that goes into a story. I'm very used to being done, and then going back and putting in stuff in the first couple chapters that I didn't even think of until VERY late in the story. Adding incidental run-ins with events early on that turned out to be significant plot devices later on.
And if you're familiar with the Final Fantasy series as a whole, you'd know that applies very closely to this series (FF10 the first exception to the rule- due to the fact that it used voice acting, which limited the mutability of the plot later). I can't tell you what the original story was without these branches and additions and convolutions, but the final product was every bit as complex as what we're pointing out here.
Back on Jenova for a second: the planet was watching it's activities. Who knows how much intelligent thought such a being can use without being "concious" as humans think of it. That'd give Jenova VERY good reason to have her cells spread throughout the human race. So that when she's ready, she'll have "sleepers" in many tiers of human life.
If she can CONTROL through her cells, she could almost certainly PERCIEVE through them. Knowing at all times everything that is happening with all of her puppets. The perfect intelligence gathering system.
But, what we CAN easily assume or just is stated fact:
1. Jenova is alien to the world. It came from the skies.
2. It isn't compatible with the lifestream, since it (or sephi, at least) is capable of traveling it without being absorbed or lost to it. Or it has such an advanced mind that the lifestream isn't capable of affecting it at all.
3. It clearly appeared with VERY hostile intent- causing cataclysmic damage and killing all nearby sentient beings.
4. Though beat into submission and trapped, it was never truly defeated.
5. The planet chose not to use WEAPON on the already beaten Jenova- and almost any of them alone could have crushed Jenova, I can only imagine what they could do as a team. So, the planet felt Jenova carried a threat so great it wasn't worth unlocking the cell to kill it.
6. I'd guess this is because Jenova doesn't need a functional body to exist, so long as Jenova cells roam free, "she" has the power to reconstitute herself and become alive again- the Reunion.
7. Jenova, reconstituted in the end. And Sephiroth, her "avatar", intend to KILL the planet, consume it's energy, and acquire the power of a "god"- then presumably move on.
8. After leaving, you could assume that both of them would go to another (or two seperate) world(s) and repeat step 1. Such a pattern could have been occuring for aeons untold before stopped.