Several kinematic chains of the upper limbs have been designed in musculoskeletal models to investigate various upper extremity activities, including manual wheelchair propulsion. The aim of our study was to compare the effect of an ellipsoid mobilizer formulation to describe the motion of the scapulothoracic joint with respect to regression-based models on shoulder kinematics, shoulder kinetics and computational time, during manual wheelchair propulsion activities. Ten subjects, familiar with manual wheelchair propulsion, were equipped with reflective markers and performed start-up and propulsion cycles with an instrumented field wheelchair. Kinematic data obtained from the optoelectronic system and kinetic data measured by the sensors on the wheelchair were processed using the OpenSim software with three shoulder joint modeling versions (ellipsoid mobilizer, regression equations or fixed scapula) of an upper-limb musculoskeletal model. As expected, the results obtained with the three versions of the model varied, for both segment kinematics and shoulder kinetics. With respect to the model based on regression equations, the model describing the scapulothoracic joint as an ellipsoid could capture the kinematics of the upper limbs with higher fidelity. In addition, the mobilizer formulation allowed to compute consistent shoulder moments at a low computer processing cost. Further developments should be made to allow a subject-specific definition of the kinematic chain.