A system includes a cylinder control module that determines target numbers of cylinders of an engine to be activated during a period, determines, based on the target numbers and an engine speed, N predetermined sequences for controlling the cylinders of the engine during the period, determines whether a transition parameter is associated with at least one of the N predetermined subsequences and selectively adjusts at least one of the N predetermined subsequences based on the determination of whether a transition parameter is associated with at least two of the N predetermined sequences. The system further includes a cylinder actuator module that, during the period, controls the cylinders of the engine based on the N predetermined sequence and based on the at least one selectively adjusted predetermined sequences.