OK we all have lists, and mine is quite large, which villains have NO reason to be attatched to their respected protagonists, or just don't really fit.
Just by naming a villain, doesn't mean the villain isn't good, on the contrary, most of them are quite awesome, but there must be a better superhero to face down the villain.
name the villain, maybe a why, and than a better suited Superhero or protagnist.
I have a LARGE list, but ill only list a few. in order
1. Mr. Mxyzptlk - This so does not belong as a Superman villain too silly, I'd say this is a MUCH Better Bugs Bunny Villain, and as far as I can tell, IT WAS. in 1943 Warner Brothers released, Falling Hare with a Gremlin harrying our beloved hare, in 1944 Superman issue no. 30 featured Mr. Mxyptlk for the first time, which was fairly similar in mannerisms. since then we have seen; Marvin the Martian, the Great Gazoo, The Impossible Man, and many others with a similar personality or plot device
2. Venom- and really all the Simbiotes they are just not right for spiderman, too creepy, too scifi, too grotesque and brutal. really belongs as a Superman Villain, or maybe the Fantastic Four or Stormwatch, green Lantern would also be good or any other hero that has a reason to be battling Aliens just not Spiderman, Its always bugged me.
3. Ra's Al Ghul - and the League of Assassins, ok this is where I bite my lip, Although I like the other two a lot, I like this one as a Batman villain a lot, but it doesn't change the fact that he doesn't belong, as a batman villain. he's too old, too ancient, always dragging Batman halfway across the globe, to some ancient ruin of some lost civilization filled with artifacts from bygone days, still being used today, even the whole global conspiracy thing isn't really batman. He and his league would be a perfect Indiana Jones Villain... but if we want to bring him into comics, Carter Hal (hawkman the Archeologist) would be a good one as well (or any archeologist or musem curator superheroes) for the more global threat, I think Justice League (pick one, they all fit) or maybe Stormwatch on a slow day