Can't say much for pre-NGC games.

FF7, (SPOILER)the ShinRa executives. The only who doesn't seem to be a sterotypical villain is Reeve and, low and behold, he's one of the main protagonists (or at least a playable character, does that count as protagonist? Also Palmer isn't really a villain, he's more an comedic oaf). Thinking about it, some of the PCs don't seem definitively to be protagonists. They're more like strays. Yuffie, Vincent, Cid, Cait Sith, and (after Midgar) even Red XIII don't really participate actively in the main quest. That is to say they don't contribute to the plot either by actions or dialogue. They don't show initiative to destroy Shinra, stop Sephiroth, or save the planet. They're all just kind of there. At least in FF8, you know why the group members continue on their quest together: they're all raised to be soldiers (apart from Rinoa who is a sorceress). Cloud's crew has motives so far removed from the main objective that you can quickly forget about them. Cait Sith isn't even real. He's a proxy. Cid is only concerned with space and airships. Vincent just wants to kill Hojo. Yuffie is completely devoid of value. Red XIII's motivation for being involved really should have dried up in Cosmo Canyon. He basically says he's tagging along because he's young and needs to see the world. It's like Rufus said when he met them: What a crew.

FF8, Raijin, Fujin, Kiros, and Ward. The storyless sidekicks of two main characters in the grand scope of the narrative. Fujin looks cool but her penchant for blurting out one-word answer AFAIK went unexplained. After Ward lost his voice, he pretty disappeared from the story and Kiros didn't get much development either. This especially sucks when it comes to characters you're playing as. Of course, compared to Squall and Rinoa, the protagonists seem kind of bland too with Zell only a marginal improvement.

FF9, my favorite character was Blank, but he's turned to stone in the first chapter and he is isn't restored until the game's end. I really wanted to know more about him. Garland also felt undedeveloped considering his apparent importance to the plot.