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.
Kain, FF4
Magus, Chrono trigger
Jowy, Suikoden 2
... these are example where it doesn't work.
I don't know who the other two are, but Kain isn't a great example. He's only an enemy for part of the game. Vaan is in your party for the whole of FFXII, isn't he? And it's not like he contributes in any way to the villain's plans. I just don't see how he could be counted as an antagonist, unlike, say, Cid or Ba'Gamnan.
Hell, as far as I can see, a Flan is a bigger antagonist than Vaan.
