I'm also a beginner, have gotten several beginner type books and am also taking lessons. Here are my thoughts:
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Uncle Tim. His strategy is to learn major scales and the chords that go with them. Basically, you spend you're entire first year doing just those scales. You spend 1/3 of your time doing scales, 1/3 doing chords, 1/3 playing songs. I'll go along with Sloth and say that playing songs isn't optimal compared to learning the chords and scales.
* Steve Vai. Nice article in a very recent Guitar World. He says you should spend 1/3 of your time doing finger exercises (including scales and pure finger exercises), 1/3 doing chords, 1/3 doing songs.
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Guitar Principles. Her thing is that too many people start with chords, scales, etc. without learning proper technique first. So their bad techniques become ingrained. So her books emphasize doing everything correctly first. You're supposed to play VERY slowly when learning scales and chords and do so without any tension. Her books don't really teach the scales and chords and are meant as an accompaniment to them--i.e., her books teach you how to practice, not what to practice. But they make good points. One of the exercises is to take a metronome set fairly slowly and switch between two chords. Surprisingly, even though I thought I had mastered the transition, I really hadn't. I really have to go in depth with this method though. I've only been glossing through it.
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Troy Stetina's metal method. I have the Lead Guitar Primer and the Rhythm method. The Lead Guitar primer teaches you the A-minor pentatonic scale and some licks. That's it. The Rhythm guitar book teaches power chords. That's it. Sounds like I'm knocking the books? No. Really, if you want to play metal, that's what you should learn first, because pentatonics and power chords form the basis for much of metal.
* Lessons. My first teacher was really haphazard. He would choose random songs for me to learn and teach me chords as they became necessary. He also didn't listen to me. Naturally, I ended up quitting him. My new teacher is a much better listener and knows that I want to learn the basics first. So he is going through all sorts of styles and teaching me lots of different chords. The problem is that, being advanced himself, he expects me to learn stuff faster than I am capable of doing. But he does listen to me and slows down when I ask.
What I am currently doing is basically the Vai method. I spend my primary time doing finger exercises, then I do the chords, both the ones I know and the ones my teacher is showing me.
The key is practice. When I first started, I was making huge progress because I would practice 2-3 hours per week. Now that I've started a new job, I'm lucky to practice 1 hour/week. If I just applied myself, I'd be progressing much faster.