There's evidence for and against this theory. Personally, I don't believe it, for reasons I can't be bothered explaining because I always get flamed if I dare to try.

I'd like to propose a new theory:

F=U!

That's right... Fujin is Ultimecia!
I've got evidence, too:

Both have grey hair.
Both of them speak strangely.
They've both got good reasons for disliking SeeDs.
Fujin was only too willing to go along with Seifer's scheme... why would she?

Think about it... Fujin's secret love/best friend, Seifer, was brought down by SeeD. He was ruined by that organisation. This lead to his eventual demise, which devastates Fujin. She inherits the power of a sorceress (possibly by killing Rinoa), and becomes Ultimecia. She just wants to be with Seifer, always... hence time compression, and possessing Edea and making Seifer her knight in the past.

It's all there, written between the lines... I may be onto something here!