Motor Imagery (MI) promotes motor learning in activities, like developing professional motor skills, sports gestures, and patient rehabilitation. However, up to 30% of users may not develop enough coordination skills after training sessions because of inter and intra-subject variability. Here, we develop a data-driven estimator, termed Deep Regression Network (DRN), which jointly extracts and performs the regression analysis in order to assess the efficiency of the individual brain networks in practicing MI tasks. The proposed double-stage estimator initially learns a pool of deep patterns, extracted from the input data, in order to feed a neural regression model, allowing for infering the distinctiveness between subject assemblies having similar variability. The results, which were obtained on real-world MI data, prove that the DRN estimator fosters pre-training neural desynchronization and initial training synchronization to predict the bi-class accuracy response, thus providing a better understanding of the Brain–Computer Interface inefficiency of subjects.