I tend to agree with The Hood about the flags - whilst they look excellent on headquarters, they do look a touch out of place on 'bus stops. The sign on the depot is good, however.
As The Hood pointed out, doing all the vehicles would be an enormous task, and would probably require a branch, since there are some people who prefer historical liveries.
As to stations - I agree with The Hood about the sorts of details that it makes sense to player-colourise: benches, lamp-posts, stations signs and canopies (and the other things that The Hood suggested). In particular, the bright red coloured lamp-posts and benches of the most modern type of railway station would benefit from being made player colour, I think (so that we're not forever stuck in the South East of England in the 1980s and early 1990s...). Some of the 'bus stops are already given player colours for their road facing signs; the 'bus stations and loading bays should probably have a similar approach to the depots.
I don't think that putting player colours on depots and stations necessarily means that player colours must go on vehicles, too; indeed, there is something to say that, for buildings, player colours are only really needed on depots and headquarters, since stations have coloured name tags in any event. However, the modern stations would look a lot better with variable colour lamp-posts...