after a few months of riding the A-C-E line in Manhattan, I've made a general observation. Usually, if a train pulls in and one car seems completely empty, you should avoid it since it probably smells like liquid garbage and fungus in there thanks to some hobo. This is a standard MTA rider habit. On the E train, you should do the opposite and look for the fullest car possible since the odds are there's some hobo causing problems anyways.
The A and C are fine, but there's just something about the E that attracts hobos, and it's awful.
I have to say that this does seem like a special reason that NY sucks. Extra-funky homeless people who live on the subway seem unique to New York. BART probably comes the closest, but SF, even with its large population of free-range mental patients, can't really compete. I don't think any other major metropolitan area, anywhere in the world, is even in the running.