Actually, with the intention of creating a cohesive feel for the national passenger services on the UK network, perhaps following the pattern of the previous SWT identity really would be the ideal way forward. I live in the former SWT region and the branding was incredibly comprehensive, but the concept of having train’s themselves being in different base colours but belonging to a greater entity really worked.
It really would be incredibly effective if local trains were red, with a few subtle blue and white accent shapes, and white doors. Regional trains could be blue, red doors and a few red and white accent shapes. Inter-City trains would be white, blue doors and a few blue and red accent shapes.
I would suggest that a new ‘one network’ graphic should be designed, probably circular overall but made up from various geometric shapes. This ‘One Network’ device would be used in its entirety on items such as the app, website, advertising, posters, pdf timetables etc. Various small sections of this graphic could be used to form the accent colour shapes on the trains, using the appropriate section of the main graphic device to create accent colour areas that are appropriate to the individual shapes of the rolling stock concerned.
The nation world end up with a very strong identity across the complete network, it would be distinctly British, but would not have the overtly nationalistic feeling of using the flag elements.