Background: Shoulder dysfunction is prevalent among recreational racket-sport participants due to high mechanical demands and insufficient proximal control. Contemporary rehabilitation emphasizes kinetic-chain coordination and dynamical-systems principles, suggesting recovery reflects reorganization of neuromuscular synergies, rather than isolated joint correction. However, evidence on sequencing effects in coordination-based rehabilitation remains limited. This study compared two exercise sequences: pelvic–lumbar coordination followed by shoulder stabilization (LS) versus the reverse order (SL). Methods: Thirty-two adult male participants with shoulder discomfort were randomly assigned to LS (n = 16) or SL (n = 16). Each group completed two 20-minute programs in opposite orders, with assessments at pre-test, post-test 1, and post-test 2. Shoulder abduction tasks (discrete and continuous) were recorded at 240 fps and analyzed using MediaPipe Pose. Joint-angle data were processed in Python and MATLAB. Principal component analysis defined dynamical degrees of freedom (DDOF), and biomechanical degrees of freedom (BDOF). Range of motion (ROM) was analyzed using two-way Analysis of Variance (ANOVA), and DDOF/BDOF using nonparametric tests (α = 0.05). Results: In discrete tasks, the LS group showed greater dominant shoulder ROM and higher DDOF at both post-tests compared with SL (p < 0.05), with no group differences in BDOF. In continuous tasks, LS demonstrated progressive increases in ROM across sessions (pre-test < post-test 1 < post-test 2), outperforming SL, while both groups showed time-related increases in BDOF. Conclusions: Prioritizing pelvic–lumbar coordination before shoulder stabilization led to superior improvements in shoulder function. Effects were task-specific: discrete tasks enhanced DDOF, whereas continuous tasks promoted earlier BDOF expansion. These findings support coordination reorganization as a key mechanism in rehabilitation. Clinical Trial Registration: ISRCTN15911792 (retrospectively registered, 30 March 2026).