The choice between the Cascade and Shift Register methods for designing pneumatic sequential circuits is a major challenge in industrial automation. This paper presents a quantitative and unbiased decision-making framework for the objective comparison of these two methods. Four distinct circuits were simulated using FluidSIM software and implemented in two industrial scenarios: an assembly cell and a packaging cell. Influential parameters, including working pressure, cylinder dimensions, valve flow rates, and hose diameters, were kept constant. Beyond calculating equipment and installation costs, air consumption, and pressure drop, novel indices—covering complexity, installation, maintainability, and economics—were defined. The CRITIC method was employed for the objective weighting of criteria, and the TOPSIS algorithm was utilized for the final ranking of the circuits. The calculations revealed that compressed air consumption was identical across all four circuits (1.62 L per cycle); consequently, energy cost cannot be considered a selection criterion. Based on the CRITIC results, maintainability and economic indices were identified as the most influential factors. In the assembly sequence, the Cascade method achieved the best performance, securing a full score of 1.000 due to approximately $250 in cost savings and ease of maintenance. In the more complex packaging sequence, the Cascade method outperformed the Shift Register method with a score of 0.917 compared to 0.073. The main contribution and achievement of this paper is the introduction of novel engineering indices and a data-driven decision-making model, enabling the optimal selection of control methods for production lines without relying on empirical judgments.