They way I see it, console characters in other games were mainly banned for consistancy purposes... Like SC2, Necrid was the only character that was banned because he was op... The other console characters were only banned because they weren't in the other games... I can't say much about SC4 though, because the other characters are available for purchase...
The balance might be horrible, but look at MvC2... That game didn't even have console characters and look how that turned out... 10 years later, its still being played, and was practically the cornerstone and bread maker for EVO, even aside from ST...