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?