More like you underestimate just how godlike certain players are.
No. It's already well accepted within the 3rd Strike community that certain mechanics make the game more balanced than what people think. The Japanese themselves have stated that parry alone makes certain matchups more fair (as in 7:3s becomes 6:4s because of parry).
Tieing into this is the fact that you only ever judge a game's balance from the highest levels of play, so if the best players of so-and-so character are playing a character at a certain level, then that level represents the true balance of the game as it exists at the moment.
Clearly, it's not a coincidence that you see almost nothing but Ken Makoto Chun-Li Yun in TOP 8 during 3rd strike tourneys (with the occasional Dudley / Yang)
It's not that other characters suck, it's the fact that these ones have powerful tools that just push them way high in the tier list.
Nobody is saying that the game is as balanced as say, SFIV (which is quite an anomaly within Street Fighter games, mostly due to how everything has been nerfed to shit). But rather, it's common knowledge among the core 3S community that the game is much more balanced than non-3S players give it credit for.