The proper way is to teach the catcher how to call his own game. This starts when you start coaching him. It's all about communication. What we look for. Why we throw this pitch to this location in this situation. The goal is to get him to the point where he can call his own game. There is no one in a better position to call a game than a catcher who understands how to do it and knows his staff. No one.
As far as pitchers shaking that just depends. If you have a pitcher that has earned your trust fine. If you have a pitcher that is a work in progress there are reasons you wouldn't want him shaking. He doesn't trust his CU so he constantly shakes it. When is he going to learn to throw it in game situations if he's allowed to shake it?
It's important for the catcher to know why we called that pitch in order to learn. It's all about communication.
Where do you want it to get to? Your catcher calling his game. The pitcher and catcher working as a team with total trust in each other. The pitcher knowing he can shake when he wants a certain pitch in a certain situation and he knows the catcher is on the same page.
As a coach this is my goal. My goal is not to have robots waiting for me to tell them to play the game. But players who know how to play the game who don't need me to micro manage the game. It's a process.