Executive Meddling: Why Vaan and Penelo exist the way they do—Vaan was originally conceived as a more rugged, world-weary and cynical character, but the developers were concerned that an older hero wouldn't go over well with Japanese audiences, since JRPGs usually have younger, Bishōnen heroes. They become proper characters in their own right in the Gaiden Games. This trope, combined with tightening the loose ends that come with six years of Development Hell is why the International version of the game is markedly different from the original game.
God Never Said That: It is a widely spread misconception that at some point, someone from Square-Enix said that Basch was supposed to be the original protagonist of the game, but was replaced with Vaan due to the Executive Meddling. In reality, nothing of the sort has ever been said. There is some degree of truth to it however, since as the above entry notes, Vaan was originally conceived as an older and more rugged protagonist, but was changed due to genre expectations, and some of those early ideas seem to have influenced Basch's character.
Too Soon: The sequence of Penelo tied up in Lhusu Mines had to be removed from the original Japanese version of the game. This was due to the game's release coinciding with the execution of a notorious kidnapper and serial killer of young girls in Japan - and they risked getting a higher rating if they included the scene.
XII has the rockiest development of any FF game to date, thanks to the collapse of Squaresoft (courtesy of Final Fantasy: The Spirits Within) and its merger with Enix, creative differences with series creator Hironobu Sakaguchi (who resigned and was replaced by Akitoshi Kawazu), and the rough equivalent of $35,000,000 US spent to make the game happen. Five years is a preposterously long time considering how Square had been producing main series FF games at a steady clip of every two years. To put it in perspective, Final Fantasy X was released in 2001, the first year of the PS2's life cycle, whilst the much-promised XII was released in the run-up to the PS3's launch and (At least outside of Japan) after the announcements of Final Fantasy XIII & Final Fantasy XV (Then Versus XIII). In fact, Final Fantasy XV is the only game in the series to have been in development for longer than XII, at ten years & counting as of 2016.
Halfway though production, Matsuno resigned from Square Enix, citing health reasons. He had lost much of his leverage after his project, Spirits Within collapsed like a bad soufflé, and Square Enix wanted to go in a more youth-oriented direction with the game's characters. Considering how much bullion they sunk into the game, you can't blame them for being a bit cagey.
As noted above, Vaan's characterization was much different. It's assumed that the original ideas for him influenced Basch.
In addition to Revenant Wings, the game was supposed to have another sequel allegedly titled Fortress. The developers making Fortress went bankrupt, but a few remnants of it survived, such as some concept art, combat storyboarding, and one amazing track.
Writer Revolt: The developers were pretty open about how Vaan was forced as the main character by the higher ups. In the final game, while Vaan starts out as the default playable character, he spends most of the time standing in the background in majority of the cut-scenes and is mostly inconsequential to the overall plot. Somewhat Vindicated by History as Vaan became popular enough in his native Japan to be the game's representative in the Versus series and later, Final Fantasy Explorers.