As an agency owner for 10 years, I can tell that almost any booking that you would do with the cruise line can be done with an agent directly. The two usual exceptions are cruises deals offered by the cruise line's casino department to big gamblers and whole ship charters.
The systems that the cruise line phone reps and travel agents use are usually exactly the same thing. Things like future cruise discounts and cruise credits are things that travel agents can handle. I had a credit from a previous cruise due to inoperable toilet in my suite, and I was able to apply the credit myself to my next cruise I am planning.
Items that we can offer that a cruise line rep cannot are:
-group pricing on most sailings if booked in advance
-additional oboard amenities
-exclusive free shore excursions
-exclusive special onboard events
-free hotel stays
-the exclusive access to one agent that is always available and can give their independent opinions.
The reservation transfer rules vary from cruise line to cruise line. Most have a specific time period that a reservation can be transferred. Once a cruise is paid in full, a reservation cannot be transferred as the agency would not be paid on it.