This is gonna be a bit of a disorganized ramble. Not really responding to anyone in particular, just getting some thoughts out of my brain.
It always made more sense to me that Sephiroth was the one in control. Even after you find out the body you were chasing the whole game was actually Jenova, everyone in the game, Cloud and Hojo most notably, still seem to regard Sephiroth as the puppet-master. Its his will, and his desire to control the clones that Cloud and Hojo bring up, not Jenova's.
Furthermore, if we were to assume that Jenova was in control, then we would have to assume that Sephiroth's mind would not actually be present in the Jenova body you chase, and that that being is just Jenova's mind choosing to appear and speak as Sephiroth. After all, why would Jenova allow Sephiroth to use her body as a vessel if she's the one in control of him.
But then that raises some issues right away, such as why would Jenova take Sephiroth's appearance and identity as her own? To manipulate Cloud? Why manipulate him at all in such a way? Its not needed for her plans to succeed. In truth the whole plan to achieve the black materia and cast meteor does not require Cloud's presence at all. Sephiroth/Jenova could have left Cloud rotting in his cell back at SHinra HQ, and the plan would have gone on just fine. The only thing Jenova would really want him for is to get back the J-cells in his body for the reunion, which she doesn't actually get in the game, so it clearly wasn't a vital part of the plan.
That would be all fine and well, but the manner in which Sephiroth/Jenova messes with Cloud during the course of the game seems to suggest a more personal vendetta, a desire for revenge perhaps. That of course implies Sephiroth is the one piloting the Jenova body, since he would have reasons to want to seek revenge on Cloud after Nibelheim. So again, it seems to me that Sephiroth is the one calling the shots. At the very least, he has enough of a say to slip his own agenda and desires into Jenova's plans.
Furthermore, if Jenova was the true puppet master orchestrating this whole thing, then why is she the one barring your path to Sephiroth in the NC, rather than the other way around. And shouldn't that control over Sephiroth have lifted once the party killed Jenova, thus restoring Sephiroth to his non-evil self? Instead he still blocks Holy, still confronts the party in a rather sadistic fashion, torturing them with his telekinesis and all that.
Perhaps you could argue that Jenova's will could survive via the cells in his body and continue to exert control over him. Fine, that would make sense. But then, what about after the final battle? Sephiroth's body has now been killed, and he is a spirit in the lifestream. Still he is restraining Holy, and laughing about it mind you. Cloud had to go into the lifestream himself to finally put an end to things. The only way this works is if you think Jenova's spirit is so entwined with Sephiroth's that they are completely inseparable even in death. But if that's the case then one must ask, is there really any difference between Jenova and Sephiroth at that point?
It makes the most sense to me to assume that either Sephiroth is the one in control of Jenova, or that the two have merged so fully that they are essentially one and the same at this point.
Sorry for the ramble. I've been thinking about this a fair bit lately, and this seemed like a good chance to unload it.
/jk) in Nibelheim due to realizing that he is "not human". Clearly, Sephiroth was invested in the idea of his own humanity. Learning of Project G may have raised Sephiroth's suspicions, to which he responded with a self-comforting denial and thus continued to believe that he was not a "monster". Sephiroth was not yet ready to accept the notion of his origins being different from normal members of SOLDIER.
It's quite simple.
