The difference is that in the entire history of WoW, rogues have only been completely outclassed in every instance of the game by every other class maybe twice, ever. They always dominate something, with one of their specs.
Operative, on the other hand, can make no such claim. They weren't even the best burst when buff stacking was around, Rage warriors were. Operative is the worst at everything they do (haven't tested healing post 1.2) and still get nerfed in every single balance patch.
Just doesn't make sense.