My view is that any travel agency is only as good as the person dealing with your request.
That said, a self booking tool or booking travel on the internet with a credit card yourself, will produce a response to your query that will be made, by definition, by a limited set of parameters; a human agent can use a much broader set of parameters and vary those parameters, according to circumstance; an API or online system cannot (well not to a practical dimension, anyway).
The reason is that, as yet, nobody has come up with a way of thinking around what you are trying to achieve.
This is the holy grail of the online travel world and known as "semantics".
Semantics, however, must not be confused with personalisation. If you wish to book a rental car, "personalisation" may offer you the best price on an Opel Astra (knowing from your input or your previous booking history what you prefer). Semantics would be knowing that, in "this" instance there are 4 of you, with lots of luggage and really what you need is a much larger estate car (aka a "station wagon" or an SUV).
Also, there are still many "wrinkles" when it comes to booking some variations of air travel as well as hotels and again, nobody has come up with a way of incorporating these wrinkles into any online or into the self-booking process. Of course, online systems or the internet will (usually) answer your question. True. But there are two main flaws - Are you asking the *right* question and are you getting the answer from the *right* source?
The greatest issue with any self booking tool (or indeed, any online booking system) comes with the danger of the editing out of opportunities from any travel policy, rather than simply placing restrictions on the systems users and of course, the DIY travel booking also edits out the ability to use an agents knowledge in order to resolve a travel event in the most cost effective manner.
Any tool which is simply designed to save money by producing the cheapest solution, is not nearly as useful as an agent. Reason? Agents tend to work on "best value" rather than raw cost.