Good practice helps with this. You can get a better sense of rhythm by playing rhythm and strumming on beat, or tapping your foot, or practicing with a metronome. You gain coordination with regular practice, and muscle memory with practicing different chord shapes and scales. the tone deafness can be improved if you always keep your guitar in tune and start to intrinsically learn what good tone sounds like as you practice.
It's tough making time for how much practice you really need to do. Really great pro guitarists like Jerry Garcia were probably playing guitar north of 40 hours a week whereas many amateur guitarists are lucky to squeeze in 20 mins a day sometimes. The best time to get great at guitar (or any skill really) is when you are a kid and really can just play 8+ hours a day every day all summer without having to worry about a job or many other responsibilities taking up limited time.
I have learned a lot over the years. I’ve had a few teachers, some better than others. I’ve used some online teaching resources. I know the fretboard pretty well, I can switch between chords cleanly and quickly, and I understand the very basics of music theory. I just can’t put it all together. None of it has become pure muscle memory.
It all takes active thinking as I play so if I’m keeping time, my chord changes are bad, if I hear lyrics, my strumming ends up matching the cadence of the vocal track.
Despite all that, I do enjoy playing what I can play. It just isn’t much.
