Practicing innovation

Try playing through scales in a cycle of 5ths/4ths in 1 position. For example, with the root on the low E, one would play the following

Key - Scale
C major - C Ionian
G major - C Lydian
D major - C Locrian
A major - C# Phrygian
E major - C# Aeolian
B major - C# Dorian
F# major - C# Mixolydian

That covers all the basic modes and makes you think about it as you go along. You should of course transpose this to different keys, start on different strings, and just basically do every permutation of it that you can think of.

When practicing scales, you can of course, do it in a multitude of ways. You could play straight up and down, or just create your own sequences. Try and come up with sequences that you've never played before because that forces you fingers to do something different so you actually develop the ability to play new ideas.

You can also take all these ideas and apply them to arpeggios. One thing I like to do is pick a key and play through all the arpeggios in the key. For example if you're playing in G major you'd have the following chords:
G major 7
A minor 7
B minor 7
C major 7
D dominant 7
E minor 7
F# minor 7 flat 5

You can play these arpeggios anywhere that you fancy, try and play them in as many different ways as you can. You should also add colour tones. One interesting thing to do is add the 2nd/9th interval. If you do this in A minor for example, you would have the following notes.

A B C E G

Compare this to the notes in A minor pentatonic

A C D E G

You'll notice that it's very similar to A minor pentatonic except rather than having the 4th interval, which is a perfect interval and doesn't sound major or minor, you now have a major 9th interval. If you were doing this over a iii chord, you'd use the flat 9 instead of the 9. This gives you an interesting sound that's somewhat like a pentatonic but more melodic, and it's a good way to break out of the whole pentatonic rut.

Another interesting idea is to take a 3 note per string scale, but instead of playing it straight through like you normally would, play the first two notes on each string and then bend the second note to the third note. This breaks out of that whole cliché 3 note per string sound, and also gives you lots of practice bending

You can also take any licks/songs that you already know and try and play them with a swing feel. This helps develop your timing and requires more control than just ripping through something with a straight time feel. One song I like to do this with is Mozart's Turkish Rondo.

You can also try playing any existing ideas with octaves. This doesn't work so well with shred style licks though

Basically to me it's all about doing things that you don't normally do, and the easiest way to do this is take stuff that you already do and turn it on its head.