> Generally, I feel like all these complaints need to be measured against what the alternative is. Which cities have a busy subway system where commuters aren't complaining?

Literally any city in Asia (or at least Japan, Taiwan, Singapore and Hong Kong, whose subway company has now branched out to run subways in many parts of the world like Stockholm). In one year of living in Nagoya the subway was late once.

That said it has a way more sensible layout than Munich where one failure in a central point does not cascade to paralyze the entire rest of the network. It is not the worst of course, since it is pretty extensive, but routing nearly every single line through Hbf or Sendlinger Tor couldn't ever have been a good idea.