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When Matsuno was in charge of the project, the intended main character was supposed to be Basch. There was debate over whether a character like Basch was marketable as a lead. After Matsuno left the project, they added in Vaan and Penelo, which were much more like FF9 characters, and Basch's role in the story was greatly reduced. As a result of all of this, the general flow of the plot really felt off during most of the game, with the best story telling being around (you guessed it) Basch's central story sections. Now considering Matsuno's track record with the Ogre Battle series, Final Fantasy Tactics, and Vagrant Story, I don't think the weaker parts of FF12 could be blamed on him. It should have been the crowning achievement of his career. I am not really sure the entire story of the game development, but I do know that much was compromised on the project.
This really explains why their characters seem to be there, but don't really have much to do with the main plot except observe it taking place - I am not one of those people who dislikes a game because they are embarrassed to play a character who is not the equivalent to the Kratos the God of War, or Venom from Spiderman (you know, a characgter who they can identify with), but Vaan and Penelo were very underdeveloped characters in FF12. Taking a look at the FF12 DS sequel, Revenant Wings, they were much much stronger (They were more reminiscent of Vyse and Aika or Chrono and Marle).
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