Designing a useful transit map is a difficult thing. There's a tradeoff between providing a useful understandable diagram of the system and providing something which more closely matches actual geography. There's also the question of how much information to provide. If there's too much it's confusing, if there isn't enough...well, there isn't enough!
The primary map provided by my local transit authority could be improved. It emphasizes the regional rail system over everything else. The trolley line routes (green) aren't completely represented, and one trolley line is left off entirely. It's even left off their map of trolley lines! On the rail lines, stations with greater service frequency, generally due to handling multiple lines, should have greater emphasis. Inclusion of certain high frequency bus lines, especially ones without close substitutes, should be considered. Perhaps just a better inner area map, leaving off the the outermost parts of the suburban rail lines, could be created to complement the existing map.