"I asked him to just stand normal with ball in glove and step to me and throw to me (no windup/leg kick or anything) and he has great control. He was nearly hitting my glove everytime. Also when he is just stepping and throwing normal he has nearly the same velocity as from a windup"
spghbaseballdad nailed it, and here's why.
First off, let's get this out of the way - trying to emulate a fully matured, seasoned athlete is impossible for a youngster trying to develop and physically grow and balance his body's muscular maturity. Don't go there.
Second - Your son is on a journey of learning how to... in addition to meeting his complex responsibilities in the center of the infield, juggling the balancing act that makes him feel confident from setup to delivery, is by no means easy.
So, combining the first and second issues, IS THEE LEARNING CURVE that your boy is going through right now. If he had the muscular maturity to manage the strength it takes to go through what others suggest to him .. do this...do that, he'd be able to adjust, there and there, and then finally come up with something that looks dynamic enough to put his movement side by side with the professionals that others think is the way to pitch.
Now here's something that goes by the boards with the majority of amateur pitchers, their coaches and the lawn chair crowd. The human body has an amazing defense mechanism. This defense mechanism goes into action ... when say, something comes flying by the face ... and then arms and hands automatically go up to protect said face. So, the same defense mechanism kicks in when the eyes spot something on the ground that the subconscious immediately recognizes as not wanting to step in, or on. Take a walk out to any amateur ball field yourself, stand on the mound in front of the rubber, then look down and the slanting surface. Is that surface telling you something? It should. It's telling you that your gonna have problems balancing yourself. Now when your son is on the mound, this kind of surface is not going unnoticed by his subconscious, whether he realizes or not. So his immediate setup posture, progress down towards his release, then his release, is in a hesitation mode. However, when he keeps an upright posture, his sense of balance and security relaxes that posture, just a bit, allowing him to do better.
I would suggest talking to you boy and asking him what he feels, physically and emotionally, with the leg kick and other styles, then without the animation. Ask him to narrate his moves, and why he does what he does. I say this because he's the one that has to learn, apply, learn again, then reapply. That's the training and learning process in this sport for any pitcher and position player. In fact, if your son is really serious about pitching, having him start a notebook of what he's learning about himself - physically and mentally, every time you play catch, he pitches, his physical workouts, and the various batters he faces.
Here's another suggestion, take video if you can from the sides, front and back, when your playing catch with your son. The human body goes through a natural set of movements when it's relaxed and with no pressure. The motion of turning the body - or not, shoulder movement - or not, and even stepping towards you during arm movements - or not, are indications of why and how he accomplishes what he does. So, if your boy is coached or instructed to do something out of the ordinary from what he does while he's relaxed doing what he does naturally (not that this may be correct) you and your son have a starting point to reason out and compare things.