The hardest part of playing the guitar for me is getting used to the fingering positions for a new piece or riff I'm playing.
Visualizing and memorizing (not merely saying "this note is here, and that note there") are a HUGE part of ANY instrument, but especially guitar.
When you learn the notes, and how they relate to keys or the sounds of chords, it makes things far easier. And like smoothasf said, focus on your weak points. If you have 20min to practice in a day, spend 15 of them on something you don't know/weak point. Then use the remaining 5 to do something you know/love...leave it on a good point till the next time you can pick the axe up.
Also, when you're practicing, you're training your mind/fingers to do certain things. So when you practice scales in conventional ways (say always starting on Ionian then onto Dorian Phrygian and so forth, your fingers will gets bias on where it's starting and stopping. Not a good idea for a person who wants to create music. Maybe it's good if you want to do the same things every time, but my mind gets complacent quickly, and I hate stopping on the root after EVERY phrase- shows lack of imagination.
Here are some ideas to change things up a bit:
1) start on your Dorian mode, and when you get to the 3rd (phrygian) in the next octave, continue up to the third on the higher register, and come down, but on the Lydian (4th) as you descend, stop and turn around and ascend again up to the fifth mode (Mixolydian).
2) Stemming from #1, practice arpeggios from different inversions/positions. But again, instead of starting from the root of say a G9 arpeggio (G-B-D-A), mix it up and start from the 3rd (B) and go up in order from there. Once you get this down, you can vary the order in a number of ways, and then when you get really good, go around the cycle of fourths (fifths) and use different arpeggios in the same method(s).
3) This next exercise, you needn't even need an instrument. Just pick one note and figure out the relationship to every key. Don't go easy on yourself, pick something odd like F#. You can mix up how you pick the relationship (cycle of 4ths/5ths, half steps, whole steps, tritones etc...). Example: F# is the 6th (Aeolian) of A, 2nd (dorian) of E, #2 of Eb and the augmented Fifth of Ab etc....
Joe Pass had a really cool idea of using scales/arpeggios and chords in one shot too...