There are plenty of amazing guitarists & musicians who have zero formal training. So I imagine you could say they picked it up the same way they'd learn a natural language. Do remember that we spend 16 or so hours a day practicing language skills, so if you played your guitar that much you might get better naturally as well.
One thing that does come to mind is working on "playing what you sing" or at least what you hear in your head, if you can do that. Think of George Benson, singing along with what he's playing. Sing an interval or phrase, then see if you can find the notes on the guitar, without thinking about scales or licks. Eventually your fingers will be able to find the notes you hear in your head without "translation" first.
Just like a speaker or writer, you have to be able to think of what you're going to say before you output the words. Otherwise, you're just stringing random syllables together.