While I agree with you, ignoring the parts where you have to play as Vaan in towns, I kinda forget he is the protagonist as I usually use other characters in the field, most other scenes have all characters in so that's fine. To me Balthier is the main character. From what we've seen with FF games, the main characters are usually clean slates with very little past but with a hidden secret revealed later. They have very little past as they learn about the world as we do but once we know about it all, the truths come out and their story is fleshed out. Cloud, Squall, Zidane and Tidus all fit this... Vaan doesn't have that 'truth' bit, Balthier does.

But is it his story. It's about how he got bought to a world and went to discover the truth about his life and father. (To end the dream). Yuna's part of it is just what she was supposed to do, defeat Sin.... but what/who is Sin?

Dang, having a hard time thinking an answer for this. Most of my favorite games let me do that.

The only one that comes to mind is playing as Zero in Megaman X3. He is way cooler than X and is quite powerful. Too bad you're kinda limited with him in the game.