Perhaps if you would have reciprocated when he was showing a lot of interest in you, the both of you could be dating right now.
You didn’t reciprocate because you are shy. However, to him, he may have actually taken that as a form of rejection.
Most guys, even the popular ones, take rejection quite personally. This may be why he has been unable to talk to you ever since.
He kept his distance when you were hanging out with your mutual friend and best friend, even when your mutual friend was talking to him.
There may be a sense of failure that arises in him whenever he sees you that often gives way to a feeling of intimidation.
As far as your body language with guys in general, you are right in that they can find your lack of eye contact or smiling as a source of intimidation.
Add the fact that you sometimes have a bored and serious look on your face and that is a recipe for most guys to keep away from you.
Your uninviting body language is the issue. It’s the reason why guys don’t approach you.