This study employs high-fidelity fluid-structure interaction simulations to investigate design optimizations for wave-assisted propulsion (WAP) systems using flapping foils. Building on prior work that identified the leading-edge vortex (LEV) as critical to thrust generation for these flapping foil propulsors, this work explores pitch control mechanisms and foil geometries to improve performance across varying sea states. Two pitch-limiting strategies $\unicode{x2014}$ a spring-limiter and an angle-limiter $\unicode{x2014}$ are evaluated. Results show that while both perform similarly at higher sea states, the angle-limiter yields superior thrust at sea-state 1, making it the preferred mechanism due to its simplicity and effectiveness. Additionally, foil geometry effects are analyzed, with thin elliptical and flat plate foils outperforming the baseline NACA0015 shape. The elliptical foil offers marginally better performance and is recommended for WAP applications. A fixed pitch amplitude of 5° provides thrust across all sea states, offering a practical alternative to more complex adaptive systems. These findings demonstrate how insights into the flow physics of flapping foils can inform the design of more efficient WAP systems.