I have no idea about how the game plays on Pro, but on All-Star I can tell you that the fastbreak is definitely an issue.
And no, User Timing is not solely reliant on how well you time the shot. If you shoot a 3 with Dwight Howard for example, and you time it perfectly, you will still miss it every single time. If you shoot a 3 with Larry Bird and you don't time it perfectly, chances are it will still go in if you're open. Ratings and timing are both taken into account with User Timing, while only rating is taken into account with Real %.
Also, sometimes shooters have off nights. So the fact that the User can be responsible for an off-game is fitting and realistic, IMO.