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.