Ignore what? The fact that his methods are exactly the same as Ganon's (attacking the Hyrule Castle and looking for the Triforce... I mean the Lightforce)?

Or the fact that his origins are basically the same (Ganon = guy gets a object of great power [the Triforce of Power] and becomes a great threat with the power of transforming into a monster [beast Ganon]; Vaati = guy gets the a object of great power [the Minish Cap] and becomes a great threat with the power of transforming into a monster [his big eye form])?

Or the fact that both Vaati and Ganon love to kidnap maiden and princesses (particularly Zelda)?

Or the fact that they're both the stereotypical bad guy who wants to conquer the world?