Interesting concept. I never really thought about it before until now.
I don't think that Squall would make a very good Seifer, if you know what I mean. Seifer had passion that you could plainly see. That's what made him so good of an antagonist. Squall kept things on the inside. It would annoy me to have a guy like that who's motivations for doing things were hidden. It made me happy to defeat Seifer in battle, because he was such a jackass (I still think he's cool). I don't think that Squall would have given me the same feeling.
I would like to say that I think that Seifer would have made a good protagonist, but I really don't think he would have. He likes to push people's buttons, and he revels in doing so. I suppose he could have been written to where it could have worked, but it would probably be hard to sell him off as the hero.
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