To me, who is calling pitches can depend on several things, many that are mentioned above.
Much depends on who you have catching and who you have pitching. I have had catchers that called pitches just as good as I would have. Maybe even better because they have the advantage of seeing exactly what the pitcher has working best that game. Also I have had pitchers that are excellent and calling their own pitches. Even then we wanted to make sure we had the ability to call pityches when we wanted, so our catchers always glanced into the dugout. sometimes we would actually make our signs easy to steal, so in a big situation we could give the other dugout a pitch different than what was coming. And we always had our bench trying to steal the opponents signs. We all have seen catchers and pitchers that actually know more about the game than the coach calling the pitches.
All that said, the majority of catchers and pitchers don't have this ability and feel for things. In that case, it is best if a coach calls the pitches. When you are at a level that you have advanced scouting reports it can really help if the catcher, pitcher and coach work together. This is where a coach has the advantage in calling pitches because he has that info at his finger tips.
Once again, I have seen pitchers and catchers get on the same page and call a great game. I have seen coaches that call a great game. Also, I have seen pitchers, catchers and coaches that have no idea what they are doing.
Actually you could go on forever talking about the reasons why coaches or catchers call a game. But most coaches that have a special catcher understand that they both are on the same page nearly all the time. A good catcher and a good coach is a great combination, no matter who is calling the pitches.