You could have still ranked Melee in the top 25 because you factor in the opponents and the margin of victory. But actual performance has to be weighed in there somewhere. Even the best team loses sometimes, but it would defeat the purpose of the voting if you said, "Well, they lost but they're still the best team so let's still rank them #1."
If you didn't consider outside information, you'd have no way of knowing that Melee's opponents in those first 4 weeks were anything special. Of course actual performance matters; this far into the season, it's by far the most important factor. And its actual performance is just as good as RE4's.
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90s games > 00s games