You have to remember that an online TA is moving truckloads of a supplier's product and they operate on razor thin margins. Some can offer a rebate of their commission in the form of onboard credit. It doesn't mean you will get customer service. The online agencies are meant for the DIYer and as such are priced that way.
I have used the Nordstrom versus K-mart analogy before to some people's chagrin when talking about the fact that I charge a consultation fee before beginning to do research on a particular cruise. You can buy the same perfume at both places yet you will pay more at Nordstrom. However people are not buying perfume at Nordstrom, but the experience.
A good cruise agent will not only recommend the right ship experience for you, but will recommend shore excursions as well. They will also have contacts at your pre and post cruise hotel if needed.
But the main reason for using a local TA (and I do have clients from all over the world) is for the same reason you get travel insurance. It is for those times you don't anticipate. Technology has allowed agents to operate from a virtual office from anywhere in the world. Building a relationship with one person either in person, or phone or email means you will be taken care of when a volcano erupts in Iceland, transportation goes on strike in Spain, or fog closes several ports along the Gulf Coast.