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An important goal of the aviation industry is the reduction of CO2 emissions. Replacement of the conventional auxiliary power unit (APU) by a multi functional fuel cell system (MFFCS) reduces the emission of carbondioxide significantly and therefore can increase the eco efficiency. However, requirements on system dynamics are higher than currently available fuel cell systems can provide. To improve the dynamics of the MFFCS especially during high peak power demands different methods are considered. This paper compares two possible methods to improve the system dynamics. The first is oversizing the fuel cell stack by solely increasing the number of cells. System oversizing is a method used for the design of conventional power supplies. For the design of a MFFCS as an alternative power supply this approach is investigated for its feasibility and extra weight. The second method for improving the system dynamics is integrating a short time energy storage. Both scenarios are compared and demonstrated by a MathWorks MATLAB simulation.