Earlier subway maps didn't combine lines that ran together, and the result was that the lines themself took up an absurd portion of the map. By combining them, you can view a lot more street-level info, which is important for navigating once you leave the subway system. Not sure what's confusing about combining them; stations explicitly state which lines stop there, and also indicate whether they are local or express stops.
To the unfamiliar, it's not obvious which lines go where. Yes, technically there are tiny numbers next to each station, but they're not as prominent as the bigger, colored bubbles, especially when you're peering at a map from a couple feet away.
You only have to watch tourists stare cluelessly so many times, get on the wrong train, go the wrong direction, etc. to understand that something isn't clear.
