hard plastic seats
https://s.hdnux.com/photos/01/23/05/56/21781404/4/1200x0.jpg inadequate climate control
I've not spent enough time on the current crop of Muni streetcars, but the old ones were horrific. They had fixed windows and really unreliable A/C. Perhaps the one saving grace of the first generation ones is that you could open the windows. BART's much worse, but the drivers will typically take note of cars without A/C because it can be indicative of bigger electrical problems.
poor maintenance leading to excessive nose and exhaust fumes in the cabin
Poor maintenance is poor maintenance. For a while Muni drivers would disable the door interlocks on the trams because the doors were so unreliable. Used to be inattentive drivers would take off without checking to see if anyone was trying to board. Ask me how I know…
extremely poor personal space
seating configurations with poor leg room
https://external-content.duckduckgo.com/iu/?u=https%3A%2F%2F...Check out that seat right by the articulation joint. Or the seats next to the stairs
convoluted routes and schedules, degrading point-to-point travel
This is a system not mode issue. BART's designed for point to point travel (mostly out of hubris really) and Muni is designed around multi-modal transfers.
the driving can be uneven, because they aren't much better off than riders
Then you've really not seen just how bad auto train control can be. When manually operated I'd run into drivers who couldn't remember how long the train was and accelerate out of a 90 degree turn and knock people at the back out of their seats. In the early 00s Muni managed to actually derail real dramatically for the same reason.
Light rail can be better but not always. Certainly the diesel vs electric issue can come into play (although you can make some truly awful trolley coaches too).