I vote for Albuquerque. We have a big bus system but it has more problem than it should. The city is 30 miles across but there are very few express bus lines. Busses run on schedules presuming jobs start at 6:30 AM and get out at 3 PM with no service in between. The bus to and from the international airport does not run on Sundays (WTF?). The bus system shuts down around midnight so all the drunks at bars drive home and get busted. It's just lame.
Minneapolis/St. Paul is about as bad as it gets. Public transit is irregularly funded, and when there is funding it's not nearly enough. Our lege still thinks they can pave their way out of the traffic congestion problem but, of course, they can't.