MGS games honestly didn't do as badly in GOTD as people think. MGS3 getting 43% on Majora's Mask isn't that bad, especially considering MGS1 probably does a good bit better.
Also, it's highly likely that SOTC was getting bandwagoned after its upset wins, so I'd say MGS2 is the only one that ends up looking really bad out of all the games there.
You're making a mistake trying to use the Rivalry Rumble to extrapolate 1-on-1 strength though. Might as well go ahead and pick Ryu > Samus while you're at it.
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