Picking the player with more potential is exactly what you do with a guy who will never see the field in year one. Its why we pick Schofield in the draft, not because he will do anything for us in 2010 but because of his potential to do something in 2011. The #3 QB is equated to a minor league system. Just like in the minor leagues teams don't just look for game ready guys, minor league systems look for guys with potential to be something a few years down the road.
If your #3 is playing you are screwed anyways considering the #3 QB doesn't even practice during the week during the season. They are relegated to trying to mimic the other teams QB for that week, which means they are not practicing the play book or the timing with the receivers. Which is a situation that doesn't exactly lead to much success in a game no matter who the QB is.