A rigorous and flexible methodology can help the preliminary phases of complex public projects by facilitating the operational steps and preparing the ground for shared acceptance. A methodology, Strategic Choice Approach, helps to shape decision problems, to design and compare feasible solutions and to control uncertainties and risks. The methodology has here been applied to support a public project in Italy, in which the technological and organizational problems were not structured by a group of stakeholder representatives, but by a more restricted working group, in the ambit of a feasibility study, and with the aim of facilitating organizational learning, communication and collaboration between the Public Administrations and the other stakeholders.