This research aims to assess the integration of different fuel cell (FC) options with battery and waste heat recovery systems through a mathematical modelling process to determine the most feasible retrofit solutions for a marine electricity generation plant. This paper distinguishes itself from existing literature by incorporating future cost projection scenarios involving variables such as carbon tax, fuel, and equipment prices. It assesses the environmental impact by including upstream emissions integrated with the Energy Efficiency Existing Ship Index (EEXI) and the Carbon Intensity Indicator (CII) calculations. Real-time data have been collected from a Kamsarmax vessel to build a hybrid marine power distribution plant model for simulating six system designs. A Multi-Criteria Decision Making (MCDM) methodology ranks the scenarios depending on environmental benefits, economic performance, and system space requirements. The findings demonstrate that the hybrid configurations, including solid oxide (SOFC) and proton exchange (PEMFC) FCs, achieve a deduction in equivalent CO₂ of the plant up to 91.79% and decrease the EEXI and the average CII by 10.24% and 6.53%, respectively. Although SOFC-included configurations show slightly better economic performance and require less fuel capacity, the overall performance of PEMFC designs are ranked higher in MCDM analysis due to the higher power density.