[q=ThE dArK oNe]During the final boss battle, I noticed the difference between the forms of Jenova and Sephiroth.The battle consists of Jenova Synthesis first, then Bizzaro and Safer Sephiroth, and finally Sephiroth himself. first its Jenova alone, then a form of Sephiroth and Jenova where Jenova is more in enforcement, then a form of the two where Sephiroth is more in control, and then Sephiroth alone.

Jenova----Jenova/Sephiroth------Sephiroth/Jenova-------Sephiroth
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Very interesting observation there... as for the other aspects of your theory, they've been fairly well discussed, so I won't add my own unnecessary opinion.

As for Sephiroth decapitating Jenova... I believe he did that simply because he couldn't find a way to free her completely from Shinra's machine. He was probably being influenced by her at the time (after all, who in their right mind would cut off their own ''mother's'' head?); Jenova knew she could survive with her body dismembered, having Sephiroth remove her head gave at least one part of her the freedom she needed to set her fiendish plot in motion...