As already mentioned, finding the best fret grouping, so your fingers can get to each note quickly and easily. In fact my biggest problem at the moment is figuring out which finger to use so the progression from one note to the next is logical.

Also mentioned was "tone". I always wondered why someone would choose to play D on the A string 5th fret when you could play an open D string more easily but perhaps you want to 'bend' or 'hammer' that note which can't be done on an open string.

As far as scales go, you will find a lot of emphasis is put on learning pentatonic scales as you can traverse up and down the strings within a fairly tight group of frets and the same positions can be transferred up and down the fretboard. Also, much more interesting than a C scale ;-)