If the clock started when the ball crossed into the court, a team could stall, for example, by throwing the ball high in the air across the gym and out of bounds without any player having a chance to catch the ball. Or, from the front court on an out of bounds play you could pitch the ball into the backcourt and stall off a few seconds, without any player touching the ball. The clock rightfully starts when an in-bounds player touches the ball.
Yes, it is often unfair that a coach's actions can influence or cost their team a game, but it is also unfair that a coach can use the referees and a T to motivate his team. I had a coach draw me closer and quietly tell me that he wanted a T. I wouldn't call it, so then he stepped back and ultimately swore at me, earning him the T. Then his team turned on the juice and blew the other team out. So, I guess it goes both ways.
A troublesome judgement call is whether a foul, typically near the end of a game, is intentional or not. The whole gym knows that a team wants to foul to stop the clock in a tight game but for some officials, if the defender is "going for the ball" no intentional foul is called. Intentional fouls carry a higher penalty in National Federation High School Rules. So it is called inconsistently. A potential rule change is instead of penalizing free throws and the ball, I would make the penalty free throws OR the ball.
Two things: 1) fans often mistake legitimate basketball moves when the player goes slowly - especially when a player down low pivots, steps and lifts the pivot foot. This is a legitimate basket move (otherwise you would never be able to shoot a layup). 2) The call most missed (maybe it is just my pet peeve) is the Jordan move of giving up your pivot foot before starting your dribble. This gives a tremendous advantage to the offensive player, and is very difficult to defend.