The trajectory tracking efficiency of a quadrotor Micro Aerial Vehicle (MAV) position controller is decreased by discrete jumps in the pose estimate provided by a localization algorithm. This paper presents a solution to this problem by first introducing a new quadrotor MAV position control architecture followed by two methods that can compensate for the jumps in the pose estimate. The new control architecture consists of Model Predictive Control (MPC) for the outer position control loop and Incremental Nonlinear Dynamic Inversion (INDI) to control the inner angular accelerations. The attitude itself is controlled with a Proportional-Derivative (PD) controller. The first method that compensates for the jumps in the pose estimate considers an adaptive control law that changes the weights in the MPC cost function when the quadrotor's position is known to be uncertain. The second method applies a filter to the reference signal before providing it to the controller. Simulations validate the proposed controller architecture and show that the adaptive controller and the controller with reference filter decrease the covered distance during a flight mission by 6.7% and 7.0%, respectively, compared to the controller without these enhancements. Therefore, the efficiency of the trajectory tracking is increased.