Well, by your definition he isn't a 'secondary villain' because he's in more than one game, but I'm fairly certain we'll see another game with Vaati.
A game could be made of the FS backstory, or possibly even after FSA featuring Vaati [his 'death' is pretty ambiguous]
Seeing as PH started out as a Four Swords game with online capabilities, but was later changed, I think it's highly possible they will come back to that idea.
They could really make a great game using the Four Swords feel to it and the DS controls/dual screen/online abilities.

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Voted as Best Zelda Theorist in the Summer '08 Awards. Thank you to all who voted, and to all who inspired me along the way!