I think I prefer TP's. It had a really amazing atmosphere and I felt the multiple forms made it more varied and exciting than WW's. Though I was blown away by WW's when I first played it. Also, TP's has the horseback segment which I really loved. You can always count on Zelda for terrific Final Bosses though. Especially OoT, SS, and ST in addition to the ones I already mentioned. They're all up there, really.
Nintendo usually delivers on good Final Bosses. It's kind of a lost art this generation, with a lot of letdowns, usually just reduced to QTEs. There have been some good ones, but I've been disappointed more often than not.
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