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1. Up and down starting and ending on root
2. Up and down, change direction randomly
3. 13 24 35 46 etc
4. Play random notes in...
5. 1234 2345 3456 etc
I learnt the major scales first, then pentatonics (2/5), then modes, then the rest of the pentatonics. So I'm still at the stage of consolidating these; arpeggios are "next" but I've basically learnt 1 of the arpeggios in one position to get me started, I didn't want to learn the rest wrong. I thought (well, still do think) there's obviously a way to consolidate the knowledge and relate the arpeggios to the scales/pentatonics so one helps the other, rather than simply being a "thing to learn" by rote.
Oh and of course, use them all the improvise or noodle around....
Then I was introduced to the 5 fret method and that changed everything regarding learning the fretboard. There is some cross over with CAGED/3NPS approaches which is useful, but for me at least, it gives a much more thorough coverage of the fretboard and it made learning all my chords, scales and arpeggios easier in 12 keys. I just wish I was shown this approach earlier!
I've deliberately been playing in various different keys, I don't seem to have any mental block on any particular key so no worries there.
Mick Goodrick talks about it in his book The Advancing Guitarist too, I think Goodrick calls it 'position playing' IIRC...
It's weighty subject but for example, learning the major scale in all 12 keys between frets 1-5. No open strings and no going past fret 5. The resulting shapes are then used across the fretboard in 5 fret areas (3-7, 5-9 etc) when learning any given key over the neck. It throws up a few extra shapes missing from CAGED and makes for a more comprehensive coverage of the fretboard (in my opinion of course!). It may seem counter-intuitive to restrict yourself to 5 frets at first, but once things get across the neck it's a real eye opener.
I work on all scales, arpeggios and most chords in this way now. I must stress, I'm not saying it's better or worse than any other method, it just works for me.
I'm curious about which shapes the 5 fret method would throw up that are missing from the CAGED method. I can see how that would happen if you view the five CAGED shapes as individual entities, but not if you view them in a joined-up way so that some patterns span more than one CAGED shape (for example three note per string scales).
I think the best bet, if you're curious, is to check it out and share your thoughts/findings.
I guess it can be thought of as a amalgamation of CAGED and 3NPS. I see that whole area as one piece of F major rather than 1 3NPS pattern and two CAGED patterns but I know they're there as for about 12 years I used CAGED and 3NPS. The 5 fret method really helped me learning all things F related (or any key for that matter) than either CAGED or 3NPS.
Page 30 of Goodrick's book discusses 3NPS (amongst other things) and how it breaks out of the idea of position playing. What I meant about the Goodrick approach was more about the amount of information that can be found in one position. Whether it's over 5 frets or 6 isn't the point, the only difference is that the range is two octaves and perfect 4th spanning 6 frets compared to two octaves and a major 3rd over 5 frets (with a lot less doubling up of notes).
I found the 5 fret method made it much more streamlined learning a lot of information...
http://i1323.photobucket.com/albums/u585/BradGuitar/5B69CB14-DA9B-4373-8FB3-579722688E25_zpsgupzugfp.jpg
I've not included diagrams for m7b5, Dim7 arps, Pentatonic, Harmonic Minor/Major, Diminished and Whole-tone scales etc...
Again, not better nor worse just another option that really helped open up my fretboard understanding. If it works for other people that is for them to give it a try and find out :-)
Having said all that I'm still on just CAGED (not looked at 3nps properly yet) so I don't know whether the "extras" are just another way of doing the same thing, or genuinely enhance the ease of doing certain things to make them super-useful (of course, its always useful to know about them in itself though).
Its a shame I never properly studied/was taught how to play the bass, since a lot of the stuff transfers over between the two and alternate positions for playing the same lines would be very useful to study as a mini-subject in itself, especially applying it to sight-reading, where you want the easiest most non-complicated approach at the tip of your fingers.
I haven't found anything yet (or any shapes) that can't be explained in terms of the CAGED system, or a least my way of applying the CAGED system. But I probably bend things to fit my way of thinking.
To steal a phrase from @viz. I love the banter.