I would have thought there would be a little more interest in giving Sephiroth a moveset. I have some animation experience in Maya from my classes at college but I haven't really done much with Brawlbox animations. I would love to help out in any way that I can. For now, I'll continue making vertex hacks though until this project gets officially rolling (if it ever actually does).
As for changing his Up Smash to his Up Throw, I have no objections to it if that's what everyone agrees on. Remember though, his grab is an impale so I think his current throw might look a little more natural from this position since he actually does it in the movie. To make things simpler to decide on, here's the two moves in discussion:
Current Up Smash
Current Up Throw
Maybe his Up Smash could be a two part hit like Link's where the first hit juggles his opponent in the air a bit with an uppercut/throw and the second hit smashes him/her upward? Just throwing out ideas here.