I believe out of all female villains, Birdo has the best chance. And even her chances are pretty low. But she does seem to be the only female Nintendo villain thats more than minor.
Aside from her, Lololo is the only other one I can think of. I'm not sure about Dark Samus, while she does seem Genderless, the Lore in the Pirate Homeworld claims it's a 'she'.
If, (an impossible If, but still an If) any Sonic or Snake characters make it in, only female villains from both series are Rouge and Sniper Wolf. Both of which aren't much, and have far more important characters.
Only third party female villain I can see from another series would be Ms. Pac-Man. I mean she is pretty villainous, picking on poor Blinky, Inky, Pinky, and...whichever that other one is. What the hell did they ever do to her? That *****.