Like other people, I first missed that this is a game where you have to choose your connections, not just a demo showing off the developer's solution.

If you want to optimize this with software you can apparently get machine-readable topology of the system via

https://www.mta.info/developers

and write your own graph traversal pessimizer for it. (Easier for stops/graph diameter maximization rather than physical distance, which I don't think is included in this particular dataset.)