Hi Claire! This is a super cool project and I'm really proud of you :)
Interestingly, your initial algorithm generated a railroad track similar to the MBTA---it was a track that was designed to connect commuters to the hotspots in the Boston area. But, now it has a lot of problems (as you probably know). Your strategy of adding an additional railroad track to connect suburban areas is super fascinating considering that those suburban connections are one of the biggest changes that people involved with railroad design are pushing for in Boston. It's one of the same things that successful rail tracks in cities like London have! (Source of my little tangent: https://www.youtube.com/watch?v=nDXsVhFG7TE)