Im pretty much in the same boat as you - I know scales but they don't sound as good as other players, but i think its important to start analizing other players solos and see how they use them to understand the why it works. Which is what I have been doing lately. For example, you probably can already play the well known Em Pentatonic scale at the 12th fret, but take the intro to Guns and Roses Sweet Child O'Mine - All it is is the Em Pentatonic. Probably a bit different than you would think to play it.

I think its important to analyze the works of other guitar greats to develop your own sound.