I would expect Mario to be on top. OoT really put Link over. He would have been strong, but not nearly as strong as post-OoT. I also agree that Yoshi, the ninjas and the shoto twins would have been much stronger in those days, as others have mentioned. I'm also tempted to say that Earthworm Jim would have been at least a solid mid-carder and that Tekken might have had a couple of decent showings in say Kazuya and Heihachi.
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SuperNiceDog had a super nice bracket too.