Sensor-based assessments in medical practice and rehabilitation include the measurement of physiological signals such as EEG, EMG, ECG, heart rate, and NIRS, and the recording of movement kinematics and interaction forces. Such measurements are commonly employed in clinics with the aim of assessing patients’ pathologies, but so far some of them have found full exploitation mainly for research purposes. In fact, even though the data they allow to gather may shed light on physiopathology and mechanisms underlying motor recovery in rehabilitation, their practical use in the clinical environment is mainly devoted to research studies, with a very reduced impact on clinical practice. This is especially the case for muscle synergies, a well-known method for the evaluation of motor control in neuroscience based on multichannel EMG recordings. In this paper, considering neuromotor rehabilitation as one of the most important scenarios for exploiting novel methods to assess motor control, the main challenges and future perspectives for the standard clinical adoption of muscle synergy analysis are reported and critically discussed.