Under appreciated and over analyzed, this game truly never got the recognition it deserved.
The characters and story are very simplistic. Why complain about it? Did anyone ever complain that the first six Dragon Quest games (Which are selling well, even now on their rereleases) have incredibly simple characters? Even the main character has no established personality, simply because he's what you think of him. He has very little impact on other characters. Why do people complain about Blue Dragon, and not about Dragon Quest? Same thing can be said about the first Final Fantasy, which I think Blue Dragon is a throwback to.
The story is simple and easy to understand. Revenge. That's the drive behind most characters. Sure, there are cliches here and there, but this late into making games and stories, what AREN'T cliches? Just because everyone else did them before doesn't mean Blue Dragon can't have it's own touch on them.
The class system is bashed for being "too customizable". Too customizable? Making the characters an all-star team with powerful abilities just because they have limited personalities is bad? Did no one play the original FFIII, which was even remade with MORE cookie-cutter characters?
With an all-star team of men in the industry, like Akira Toriyama as artist, Nobuo Uematsu as composer, and Hironobu Sakaguchi, the creator of Final Fantasy, as head of Mistwalker, this game definitely was bashed too hard and not appreciated for what it was...
Old-school RPG goodness.