One way to systematically identify customer pain points is to do what's called Journey Mapping. This involves thinking about every stage of a transit's customer's journey from planning their trip to the "last mile" egress to their destination.

For each stage we ask ourselves what do customers see, what do they hear, what do they smell, and what do they feel. This helps us identify the pain points we need to remedy to make it a great experience.

We also think about the diverse needs of diverse customers, so for example a mom with a stroller traversing the system, or a person who can’t afford a smartphone with a data plan and how they access real time information, or how a customer who is blind navigates a train station - just to give a few examples.

The best way to conduct Journey Mapping is through "in-the-moment" interviews. This involves randomly recruiting riders, paying them an incentive to participate in research, and riding along with them. Alternatively, you can interview riders by phone or web after their trip. This is much less costly, but a customer's ability to recall details of their experiences will rapidly recede. It's much better to interview them in the moment so you can detect friction they might experience or moments when they feel anxious or confused.
After the customer interviews, overlay key observations onto a Journey Map like the one above to paint a picture of the whole journey and pinpoint pain points. You can also create graphs that depict the emotional state of riders through the various journey stages to identify highs and lows, and find moments when customers are anxious, confused, or uncomfortable. Once you have Journey Maps, convene subject matter experts in your organization - especially those who are directly involved in service delivery - to share the Journey Map illustrations, develop CX solutions, and identify and resolve obstacles to improvement.
Tip:
Video record your customer interviews, and ask them to sign a release form. The footage will be useful when presenting the research results. There is nothing more powerful than learning new insights directly from customers!