Bill compiles quite a list of outstanding issues, from the T's continued inability to figure out how to get them to work on commuter rail to the amazing way they've made fare evasion so easy:
... Fare evasion was somewhat of a rare sight for prior to the introduction of the AFC system, but now it's something you don’t have to look around to find. Three, four or five people going through a gate at once on a single tap of a single card occurs constantly. Evaders forcing their way past people as they open a gate to exit is something that happens frequently as well. ...
Other cities have implemented gate systems that have successfully kept fare evasion under control. The T spent millions on a custom solution that has turned evasion into an epidemic.
He also discusses ongoing delays in station reconstruction projects along the Green Line.