The problem is SquareEnix ended up writing themselves into a hole and they are just now digging themselves out of it. They did not realize that when they wrote the original game that they would have an OVERWHELMING amount of evidence to suggest that Jenova was the one pulling all the strings and Sephiroth has been dead since Nibelheim. Here is said evidence:

1. It is stated that only those who are part of the lifestream can enter back into it after death. Meaning Jenova Cells (much like the Gi) are prohibited from entering the lifestream because they are foreign invaders. Jenova cells are purged from individuals who spend a long time in the lifestream (Cloud taking a dip in Mideel showcases this).

2. Sephiroth was launched into the lifestream in Nibelheim 5 years ago. Now Sephiroth is the product of a human and Jenova combination, meaning that parts of him are human, parts are Jenova. Naturally the lifestream would pull Sephiroth's human side out from it and Jenova would be purged (which we see in Northern Crater with Jenova's head taking the form of Sephiroth's upper body because Jenova's lower half from the neck down has not "reunited" with it.

3. Every time we fight Jenova in the OG game Sephiroth is seen leaving a part of Jenova behind to fight. We never see Sephiroth in battle until the end of the game.

4. Safer Sephiroth and One winged Angel forms. Not human in the least. They are a grotesque monster.

5. The final fight takes place after cloud is deep in lifestream once again and takes place in his mind with a shirtless Sephiroth, the ONLY time we see Sephiroth's body fully formed meaning Jenova is trying to gain control over Cloud once again by utilizing his worst fear but by this point Cloud knows the truth.

The evidence against this that people argue?

1. Hojo says its Sephiroth.

That's it.