I'm not an expert on this but John Elway is and he commented publicly on Tebow's mechanics problems.
Tebow's problem is in the footwork and squaring his shoulders. If the feet are properly aligned after his three step drop then his body is properly aligned and the throw will go where his body is pointing. Accuracy depends on this. Having to THINK about getting into the proper position is fatal. It's like golf. If you have to think about your swing, you can't develop any consistency.
When running with the ball you need to stop and plant to throw accurately downfield -- at least if you're throwing more than just a dump-off pass.
Being able to do these things accurately requires endless practice. Orton has been practicing from under center for 10 years now in College and the NFL. Tebow came to the NFL with virtually NO such practice since he operated from the shot-gun in the spread offense at Florida and it shows.
It's by no means certain that he can EVER really master those skills adequately, but we'll see.