It's well organised, it runs very frequent trains, it's pretty clean. Good transport system and nothing wrong with it, and it makes getting round the city a million times easier than a car, and significantly quicker than the bus.
But the people on it are all fecking miserable!
But the trains are tiny! It is sometimes not even possible to stand upright in them!
It's "technically" fine, but large parts are also substantially over capacity during rush hour, and full of people who often are either well into a 1h-1h30 commute in the morning, or dreading one after a long day in the evenings. Once you get out of zone 1/2 things are generally a lot more pleasant.
And you see a massive difference on many of the commuter trains as opposed to London Underground - come weekend, for example, a lot of the commuter trains have a relatively cheerful atmosphere and a lot of people breaking out a beer or wine and relaxing, for example...
Travel on the Underground outside of rush hour and the atmosphere is a lot more pleasant (though Londoners will still try exceedingly hard to avoid eye contact with you).
I take back what I said.
Edit: but seriously, the subway is a lot of what makes living in a city bearable, or even what makes it better than living outside a city. I would take a 40 min commute on a train over a 40 min commute in a car any day.