My personal best take is that Sephiroth is 'in control' so much as he is the one deciding on all the actions. However Jenova is not so much a manipulator of actions, but is behind the scenes subconsciously tweaking Sephiroth's motivations.

So Sephiroth's plan is his own, but the reason he wants to do it in the first place is because of Jenova messing with his head.