I think most of us were introduced to scales soon after we picked up the guitar. Shortly thereafter, we were warned to not let learning scales dominate our practice time...I certainly was.

This video from the great ( :) ) Justin Sandercoe of justinguitar.com adds some meat to the reasoning, "you shouldn't learns scales (if) you don't know what you're learning them for."

On the other hand as Justin points out, don't discount the gain in flexibility, picking, coordination, technique, etc., gained from running through the five positions. THAT was my motivation when I started practicing major and minor pentatonic and, happily, when I hit GT lessons that called upon those capabilities I could concentrate on the *music* rather than building my muscle memory, i.e., my skill level was more than ready for those lessons.