Wouldn't know which one it is, but I've heard complaints about the Ikari warriors port on the NES, but I'm not sure how much truth there's to that. It would also depend what you mean by worst. I don't remember KoF Sky Stage been kindly looked upon. It also depends on your definition of worst. I mean there's people that said Doki Doki Majo Shinpan was horrible because think of the children, 2D = 3D, muh objectification. Also according to the people that made the petition a while back demanding that SNK Make a XIII UM called XIV pretty crap and an insult in the same petition (which we know isn't true since objectively speaking it's a solid game), There's also XII which was bare bones as fuck, or 2001 which not looked at kindly by some either, etc, etc. As I said it depends on your definition of worst.
C'mon man. Every company has their bumps SNK is no exception.
Jaxon Flores
2001 is pretty crap and unlike many doesn't have graphics or music to save it. Also, I retried 2000 and the input interpreter is crapastic, dp motion have priority over everything, leading to qcfx2 motion needed to be done super slow.
Ryan Clark
Worst to me would be something seriously flawed in gameplay. Not really something like DDMS, unless that plays like crap. I'll have to try out 2001 then. I don't remember 2000 being that bad when I played it, but it has been years since then.