This paper aims to improve the interaction and coordination between the human and the robot in cooperative execution of complex, powerful, and dynamic tasks. We propose a novel approach that integrates online information about the human motor function and manipulability properties into the hybrid controller of the assistive robot. Through this human-in-the-loop framework, the robot can adapt to the human motor behavior and provide the appropriate assistive response in different phases of the cooperative task. We experimentally evaluate the proposed approach in two human-robot co-manipulation tasks that require specific complementary behavior from the two agents. Results suggest that the proposed technique, which relies on a minimum degree of task-level pre-programming, can achieve an enhanced physical human-robot interaction performance and deliver appropriate level of assistance to the human operator.