The Cooperative Research Centres (CRC) program has become the dominant model for "triple helix" cross-sector R&D cooperation in Australia. By comparison with more specialised programs in other countries the CRC program covers a very broad range of fields and objectives and might be described as a "jack of all trades". We argue that this "one size fits all" approach has become a limiting factor in the further development of cross-sector collaboration. Based on a range of prior empirical studies of CRCs we explore the environmental factors which shape the organizational structure of CRCs and identify the points of flexibility required to accommodate the range of missions and structures observed within the centres. Four broad influences are important in shaping the structure of CRCs. These are the changing policy focus of the CRC program; the diversity of missions, objectives and outputs of the CRCs; the expectations of researchers within CRCs which emphasise scientific careers and collegiality; and complementary changes in the innovation system which have led to a diversification of collaborative research. We conclude that the mature CRC program must take on a reinvigorated role and we make specific proposals to ensure that CRCs continue to lead the innovative organization of cross-sector research in the future.