Clearly mark all bus stop "zones" on the street and enforce illegal parking within bus stop zones downtown. When vehicles park "in" bus stops the visibility of waiting riders from a bus operator's view point is diminished. If they can't see you they end up driving right by. This is especially true of taller vehicles. This may require co-ordination with the police.
Background: I have been driven by without being picked up while waiting for the westbound 4 and 22 on 6th and Nueces 3 times because a truck was parked in the bus stop. This was even despite me frantically waiving over head with both arms. The truck is on a regular schedule and I have learned to wait in the street for the buses while also waiving both arms. Waiting in the street is probably a safety issue and potential legal nightmare.