An agency should get back to anyone who files a complaint within 24 hours so they know the issue has been received and is being dealt with.
When someone complains, they should be able to keep track of their complaint (online would be fantastic). For that purpose, the agency should assign a case number to each complaint and furnish that to the complaining party. MARTA does this and calls the number a HEAT number.
The ability to offer feedback is very important. Some agencies do better than others. Prince George's County (MD) Transit does not post any information about how to provide feedback on their website. However, they do have a person responsible for receiving that feedback. Putting his name and email/phone on the web would be a great start.
Agencies should appoint an ombudsman who can represent the interests of riders when they submit comments, questions, or complaints. S/he would be responsible for investigating rider complaints and responding to comments.