Eh, historically speaking Zelda villains that leave an impact are pretty rare. It's mostly just Ganon, and then Majora/Skull Kid and Ghirahim.
Let's be real, people mostly mention Vaati because he's the only other recurring villain besides Ganon, he's not terribly interesting in his own right. Does anyone care about guys like Bellum? Or Nightmare? People mostly ended up disappointed with Zant's role in Twilight Princess (even though I thought he was at his most interesting as a kooky weirdo). Link's Shadow from Zelda II is mostly, well, oveshadowed by Dark Link. You get the idea here.