All too often I see beginners, even teachers teaching beginners, put the priority on the timing first... they strum in time, switching from one chord to the next regardless of whether they are fretting properly.... thinking that with enough time and practice, they will "work out the kinks". What is really happening is a conflict in your head where the feedback from your left hand says "ahhhh! I don't have this fretted properly, I'm not ready!" and yet you tell yourself "go ahead and strum anyways, because you need to STAY IN TIME!". You're essentially telling yourself that bad fretting is ok. Yes, with enough effort and practice you can get the chords sounding cleanly, but its far faster to first practice the chord changes first without the metronome, focusing on just playing the chords cleanly, and making the transitions smooth. Once you have that down, add the metronome at a slow tempo and practice changing chords in time.
The other is learning riffs, scale sequencing, arpeggios, hammer-ons etc. Again, turning the metronome off and just getting the mechanics down, then getting the "feel" of the riff or whatever can be really helpful. When you feel like you've got it, then put the metronome on and practice in time.
The bulk of practice should be done with a metronome. If you are going to run through all five patterns of a major scale for example, you should be doing that to a metronome. When you're jamming, coming up with riff ideas, that should also be done to a metronome. If you're one of those guys that says "I hate practicing to a metronome, it just throws me off" then you know you're in trouble.
