One pet peeve that gets to me is something that's done on a lot of commuter railways and S-Bahns, the 10/20 minute schedule. The schedule looks like:
2:10
2:20
2:40
2:50
3:10
etc, when it should be like this:
2:10
2:25
2:40
2:55
3:10
This minimizes waiting and allows for frequent service every 15 minutes.
What are your pet peeves?
This isn't 100% public transit's fault, but I hate how expensive living anywhere that has even a little public transit is. Despite the old stigma of public transportation, the truth of the matter is that here in the US: the poor drive cars and the rich live in walkable cities with public transit.