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Require transit users to fill out a library card like system to get onto the trains. If you want a guest pass, you'll have to submit to a retina scan.
This way, if people piss in the cars or try to sell people shoes, or bullshit like that, you can permaban them from the subway system and they won't be able to ban evade.
Then just invest in a lot of CCTV and transit cops, and slowly but surely get rid of all the hucksters, beggars, homeless, drug addicts, mentally ill, and other people who make riding the subway unpleasant.