For a cautionary tale of what could happen if you make your subway system too complex, you might want to read the classic science fiction story, A Subway Named Mobius (http://www.rioranchomathcamp.com/Topology/SubwayNamedMobius.pdf). Here's one introduction to the story:
The principles of connectivity state that as a system makes more connections to other parts of itself, the connectivity of that system increases in an exponential fashion to staggering levels. The subway under Boston had been growing in complexity for years. It was so complex, in fact, that the best mathematicians could not calculate its connectivity...
Thanks for directing me to this - now I know why the subway/el trains appear and disappear like ghosts in the game ;)
That was a great story! Very interesting.