The advance in control engineering education needs well-designed studies that validate what methods and tools work best. This paper addresses the lack of empirical evidence supporting innovations in control engineering education by proposing a methodology that works at different abstraction levels. Hence, innovations’ impact on students’ performance can be statistically analyzed either globally or locally by examining competencies or fine-grained indicators, respectively. The article reports the application of the methodology for evaluating an interactive simulation tool, named LCSD, on 101 students at the Pontifical Catholic University of Valparaiso in Chile. According to the experimental results, LCSD is an effective free alternative to enhance the student’s skills on control system analysis for our automatic control course. Also, some improvements have been identified for future LCSD versions.