I’ve ridden dozens of transit systems across four continents (I happen to collect transit means of payment as a weird hobby). Smelling urine is not a regular occurrence for me on the L or 4/5/6. Which lines do you usually ride? There are a lot of them and I know the experience varies.

I rode the A and the 2/3/4 lines usually. Try standing near the edge of the track. You'll get a whiff. It's not just that either, there's also a ton of litter and way more homeless people in the system than I've seen anywhere else. It's unhygienic to the point that it's a joke to New Yorkers not to get on a train car that's empty. Never seen that elsewhere.

Of course the state of the subway is a reflection of the city as a whole rather than an isolated issue, and that's true everywhere in my experience.

If you ride the Bart seeing urine is quite normal, along with the producer sitting in the middle of the puddle.