Ecosystem-based fisheries management (EBFM) seeks to integrate the full complexity of real-world marine ecosystems into the design of fisheries management policies and regulations. EBFM is practiced currently with the help of complex ecosystem process models that track and simulate numerous ecosystem elements/organisms across space and time. For simplicity and to maintain tractability, the fishing sector component of process models maintain restrictive assumptions for harvesting technologies, fishing behavior, regulations, and fishing sector response to changing stock conditions. Predictions of fishing sector-ecosystem interaction obtained under these assumptions can grossly misinform EBFM policy design. An alternative rational fishing model is presented and applied to the Gulf of Mexico commercial reef fish fishery. The model relaxes the restrictive assumptions currently in use highlighting stark differences in ecological and external validity across modeling approaches. While models of rational fishing are data and computationally demanding, results show that improved validity they deliver may be essential to further advance the EBFM paradigm.