Imbalanced overall, or unique cases?
Overall, Street Fighter III. SF3 was never a bastion for balance, and balance did get better as they went, but yeah... Second Impact was hilariously broken to a whole new degree. Ibuki and Sean were the top, top, top, tiers in that game, especially Ibuki. Ibuki was so hilariously broken it wasn't even funny. Touch of death combos, pokes that beat everyone, crazy safe and powerful... You name it, she had it.
Third Strike was a bit better, but mostly it was a power coup. Instead of Ibuki and Sean it was all about Chun Li and Yun (with honorary mentions to Ken and Makoto). Chun had the best pokes in the game by far (half the cast can't do anything but whiff punish), everything she did was safe, her super had two bars, wasn't too big, and was insanely damaging WITH possibility of follow up. Yun was the other beast: A divekick, great pokes, fast, and the best super in the game by far: Genei Jin. "Steroid" kind of super that made Yun faster and allowed him nearly endless juggling ("hup, hup, hup, hup, hup..."). Best part? He built meter crazy fast and had the shortest super bar in the game! Basically more than half the match you were fighting Genei Jin. Any hit usually resulted in half your health going away.
In a "unique" case: Street Fighter II: Super Turbo. SFII wasn't a very balanced game either, but Akuma, who first became playable in ST, was broken beyond reason of belief. He was never meant to be played competitively, and you can see it when you use him. His air fireballs simply destroy everyone. On top of that he had insanely high damage, inescapable and unblockable "resets" and setups, and he was the only character that could not be stunned. He was hard banned from tournament play for a very good reason. Even "old" Sagat looked wimpy next to him.
Then again, Third Strike had Gill...