Real % does not factor in timing at all, actually. It simply uses the ratings and decides if the shot should go in or not.
I prefer User Timing because it takes into account not only the players' ratings, but also the users ability to time the release of the jumpshot. This combination makes the user feel much more in control.
As to your comments on fastbreaks "not being an issue", I whole-heartedly disagree. Yes, teams are supposed to push the ball up-court after a defensive rebound, but at default almost every team relentlessly pushes the ball up court and takes the first shot possible, even if the ball-handler is completely covered and the shot is a terrible one.
You have to lower the Fastbreak sliders in order for the CPU to only push the ball up-court and to take the first shot available when it makes sense to do so.