I'm 99% positive Black Widow is not going to be a villain. Plus, having multiple villains isn't the problem, it's how they are handled. Batman Begins had: Ra's Al Ghul (should have been pronounced "Raysh," but whatever), Scarecrow, the mob, and corrupt cops. The Dark Knight: The Joker, Two-Face, Scarecrow, the mob, and corrupt cops. Both those movies are fantastic and feature more villains than any other comic book movie.

Something like Spider-Man 3 is an example when the director and writer couldn't decide on how much screen time each villain should get and you get a huge cluster of shit.