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This paper illustrates a methodology developed to facilitate the analysis of complex systems characterized by a large number of technical, economical and environmental parameters. Thermo-economic modeling of a natural gas combined cycle including CO2 separation options has been coupled within a multi-objective evolutionary algorithm to characterize the economic and environmental performances of such complex systems within various contexts. The method has been applied to a case of power generation in Germany. The optimum options for system integration under different boundary conditions are revealed by the Pareto Optimal Frontiers. Results show the influence of the configuration and technical parameters on the electrical efficiencies of the Pareto optimal plants and their sub-systems. The results provide information on the relationship between power generation cost and CO2 emissions, and allow sensitivity analyses of important economical parameters like natural gas and electricity prices. Such a tool is of interest for power generation technology suppliers, for utility owners or for project investors, and for policy makers in the context of CO2 mitigation schemes including emission trading.