I would agree with many of the earlier comments but go on to say that perhaps you should continue to use scales as a warm up exercise, but shift the focus of your study on to arpeggios for a while. Since you are already thinking of applying scales against a chord or key center, arpeggios will help open things up.
The best resources for doing this will take you in a Jazz Fusion direction but that can only be a good thing. I would also recommend you grab the Frank Gambale Technique book - Frank's approach to guitar is highly logical, thorough and methodical. He covers using intervals, triads, 4 note arpeggios, pentatonics, dual triads and scales. There's two books in the series but book one will take you 6-12 months and will give you a massive amount of ideas to process.
After that, go to TomQuayle.com website and dive into some of his downloadable lessons. When you want to break out of the Pentatonic/Diatonic rut and start finding ways to play 'outside', I can't recommend Tom's lessons enough. It's very much Jazz theory, but put into a very modern context.
To SpaTans point, I once learned a great technique from Prof David Baker - horn players can't twiddle endlessly like piano players and guitarists because they have to breathe. So try taking a breath and silently exhale or speak while you play - when you run out of breath, stop playing, take a breath, and start again.
A long time ago, I got picked out of a crowd of 300 guitarist (by the aforementioned Prof Baker) to come up and jam with him (at a Sydney School of Music summer camp). I was hella nervous to say the least... But I remembered his advice and took a deep breath, imagined myself yelling at my girlfriend (who was, to be fair, a total lovelovelovelovelove...) and unleashed a tirade of notes, phrased like a one-sided argument. By the end of the number I got an ovation and the Prof said "I like this kid, he plays the blues dirty!". For the rest of the summer I was known as "Dirty". Cool advice from a jazz god.
