I think people over exaggerate Marvel's "villain problem".
Marvel's track record with villains isn't any worse (and arguably better) than any of the other comic book franchises, with one major exception. The exception is Batman, which has had a number of great villains. Batman has by far the best villains in the comics, so it should come as no surprise that he has the best villains in the films too. But if you look at Sony, Fox, or non-Batman DC films, the situation is similar to Marvel.
Marvel has ONE truly great villain, Loki.
Fox has ONE truly great villain, Magneto.
Sony has ONE truly great villain, Dr. Octopus.
DC, not counting Batman, has ONE truly great villain, Terence Stamp's General Zod.
Then there are villains that are still good, but not at that level (the Pierce, Stryker, Dafoe's Goblin, Lex Luthor types).
And those that are crap, like Malekith (although he is more dull than horrible), Dr. Doom, Electro, Parallax, etc.
The only reason it is an issue with Marvel is that they get so much else right. There is nothing to really complain about with their heroes, so all the negative attention gets focused largely on the villains whereas the criticism is more spread out when it comes to the other three companies.