Well, I currrently have SSBM ahead of SM64 (though I notice most people don't). But if SM64 beats CT, obviously it would move ahead of SSBM. So, a loss to SSBM would be worse, if it were by the same margin, although that's somewhat offset by CT/SM64 being a direct matchup and more recent a match. SM64 also has wins over SMB3 and SMW, whereas CT has wins over SMB3 and LTTP, but CT's wins were by much larger margins. So I guess the losses side would be a push, but CT would still be ahead on the wins side.
So, I'll probably still vote CT #1 unless it loses by a substantial margin (say, 4 votes).
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90s games > 00s games