I think it was because they didn't think he'd appeal much as a protagonist. Stupid reason I know, but...
Yeah, they didn't want to try to use an older guy as a protagonist, after the last game they tried that in (Vagrant Story) failed. Also, Vaan is more of a viewpoint character than a main character, and coul actually be called more of an antagonist than a protagonist, as he is instrumental in the character development of Baltheir, Ashe, and Basch.
Isn't an antagonist a villain?
Not necessarily.