I'm from the "Jenova cells float in the Lifestream still" camp, myself. Also of the "Jenova cells in Geostigma survivors" camp.
The creators haven't stated otherwise to my knowledge, and the narrative makes it hard for me to believe the cells could diffuse that easily into the Lifestream and cease to be unique (there wouldn't have been an issue getting rid of the bitch 2000 years ago then
). They might be inert at the moment with no consciousness to direct them, but if a strong enough will came along with the capacity and opportunity to start, they could still be a problem. By themselves though, that's more sketchy. I suppose it would be a question of what the cells are capable of doing when enclosed in a host and not directed directly.
Also went and rewatched that
'Seekret Ending' again and think it's safe to say Genesis isn't waking up on his own. He's pretty unphased by recent events and doesn't react to Weiss' presence until some electrical shit decides to conduct from Weiss' body to the surrounding stalagmites and then to Genesis' water-bubble-thing. So Minerva holds some weight on his I-am-the-last-hero-to-protect-the-Planet thing and must have very limited options. (Which I guess is true, since the heros of the last game killed off all her WEAPON and Omega got HEADSHOT'd by some goth guy.)
Personal opinion: If Jenova or Jenova cells aren't involved with what's going to go down now, I'm going to be sorely disappointed.
ShinRa Company's washed up on the shore (and apparently Rufus pulled out his Evil Stick anyway), Sephiroth would be pretty redundant, and if they 'reveal' another group of super soldier labrats that have been somehow hiding underground/in a cave/on an invisible sky continent since forever I'll scream.
Snarky post is snarky. And I can't believe I typed directed directly and was serious...