Previous studies on Eye-Hand Coordination Training (EHCT) focused on the comparison of user motor performance across different hardware with cross-sectional studies. In this paper, we compare user motor performance with an EHCT setup in Augmented Reality (AR), Virtual Reality (VR), and on a 2D touchscreen display in a longitudinal study. Through a ten-day user study, we thoroughly analyzed the motor performance of twenty participants with five task instructions focusing on speed, error rate, accuracy, precision, and none. As a novel evaluation criterion, we also analyzed the participants’ performance in terms of effective throughput. The results showed that each task instruction has a different effect on one or more psychomotor characteristics of the trainee, which highlights the importance of personalized training programs. Regarding different display technologies, the majority of participants could see more improvement in VR than in 2D or AR. We also identified that effective throughput is a good candidate for monitoring overall motor performance progress in EHCT systems.