Cori hated the shonen-protagonist personality in general, I think. If Yugi had been a brash, slightly-dim jock rather than a short, socially-awkward nerd, she'd have hated him as well. (I'm presuming she didn't hate him?)

So... I'm presuming the ships would be manly!Joe/woobie!Sora, artsy!Matt/Mary Sue [whether Mary-Sue is named Mimi or not], T.K./Kari, Ken/Mary-Sue!Yolei, Tai/nobody, and Davis/nobody? :( Oooh man.

And Wizardmon/Gatomon, of course. Except she'd wreck the ship like she wrecked Rocketshipping. *sigh*