If you're really serious about learning theory start with the Major Scale and make sure you memorize all the different patterns as well as the positioning of the whole-steps and half-steps. It's important to get as comfortable with the major scale as possible, learn it inside and out so you can play it in any key on any part of the guitar neck with barely any thought at all. Then once you can do that, start learning modes and minor scales, but don't rush into them cause the better you know the major scale the easier it'll be to learn modes and a few other scales as they are related to the major scale... For example:
Major Scale = 1 2 3 4 5 6 7 1
Natural Minor = 1 2 b3 4 5 b6 b7
So if you know the major scale extremely well then the Natural Minor scale should come fairly easily as you just have to lower a couple notes in your major by a half-step.
Also, like everyone else is saying, practice, practice practice... Push yourself to play things that are "impossible" and don't just stick to playing music you love, learning genres you're not a big fan of will teach benefit you alot... and buy Victor Wooten's - "The Music Lesson", it's a book that goes over all the basic/obvious aspects of what makes up music and even though you already "know" everything in it, it will completely inspire you if you're anything like me or feel "stuck" in any of the ways I used to!
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