Energy system models allow the development and assessment of ambitious transition pathways towards a sustainable energy system. However, current models lack adequate spatial and temporal resolution to capture the implications of a shift to decentralised energy supply and storage across multiple local energy vectors to meet spatially variable energy demand. There is also a lack of representation of interactions with the transport sector as well as national and local energy system operation. Here, we bridge these gaps with a high-resolution system-of-systems modelling framework which is applied to Great Britain to simulate differences between the performance of decarbonised energy systems in 2050 through two distinct strategies, an electric strategy and a multi-vector strategy prioritising a mix of fuels, including hydrogen. Within these strategies, we simulated the impacts of decentralised operation of the energy system given the variability of wind and across flexibility options including demand side management, battery storage and vehicle to grid services. Decentralised operation was shown to improve operational flexibility and maximise utilisation of renewables, whose electricity supplies can be cost-effectively converted to hydrogen or stored in batteries to meet peak electricity demands, therefore reducing carbon-intensive generation and the requirement for investment in expanding the electricity transmission network capacity.