The performance of multimodal mobility systems relies on the seamless integration of conventional mass transit services and the advent of Mobility-on-Demand (MoD) services. Prior work is limited to individually improving various transport networks operations or linking a new mode to an existing system. In this work, we attempt to solve transit network design and pricing problems of multimodal mobility systems en masse. An operator (public transit agency or private transit operator) determines the frequency settings of the mass transit system, flows of the MoD service, and prices for each trip to optimize the overall welfare. A primal-dual approach, inspired by the market design literature, yields a compact mixed integer linear programming (MILP) formulation. However, a key computational challenge remains in allocating an exponential number of hybrid modes accessible to travelers. We provide a tractable solution approach through a decomposition scheme and approximation algorithm that accelerates the computation and enables optimization of large-scale problem instances. Using a case study in Nashville, Tennessee, we demonstrate the value of the proposed model. We also show that our algorithm reduces the average runtime by 60% compared to advanced MILP solvers. This result seeks to establish a generic and simple-to-implement way of revamping and redesigning regional mobility systems in order to meet the increase in travel demand and integrate traditional fixed-line mass transit systems with new demand-responsive services.