Unlike RequestFactory which has poor error handling and testing capabilities (since it processes most of the stuff under the hood of GWT), RPC allows you to use a more service oriented approach. RequestFactory implements a more modern dependency injection styled approach that can provide a useful approach if you need to invoke complex polymorphic data structures. When using RPC your data structures will need to be more flat, as this will allow your marshaling utilities to translate between your json/xml and java models. Using RPC also allows you to implement more robust architecture, as quoted from the gwt dev section on Google's website.
"Simple Client/Server Deployment
The first and most straightforward way to think of service definitions is to treat them as your application's entire back end. From this perspective, client-side code is your "front end" and all service code that runs on the server is "back end." If you take this approach, your service implementations would tend to be more general-purpose APIs that are not tightly coupled to one specific application. Your service definitions would likely directly access databases through JDBC or Hibernate or even files in the server's file system. For many applications, this view is appropriate, and it can be very efficient because it reduces the number of tiers.
Multi-Tier Deployment
In more complex, multi-tiered architectures, your GWT service definitions could simply be lightweight gateways that call through to back-end server environments such as J2EE servers. From this perspective, your services can be viewed as the "server half" of your application's user interface. Instead of being general-purpose, services are created for the specific needs of your user interface. Your services become the "front end" to the "back end" classes that are written by stitching together calls to a more general-purpose back-end layer of services, implemented, for example, as a cluster of J2EE servers. This kind of architecture is appropriate if you require your back-end services to run on a physically separate computer from your HTTP server."
Also note that setting up a single RequestFactory service requires creating around 6 or so java classes where as RPC only requires 3. More code == more errors and complexity in my book.
RequestFactory also has a little bit more overhead during the request processing, as it has to marshal serialization between the data proxies and actual java models. This added interface adds extra processing cycles which can really add up in an enterprise or production environment.
I also do not believe that RequestFactory services are serialization like RPC services.
All in all after using both for some time now, i always go with RPC as its more lightweight, easier to test and debug, and faster then using a RequestFactory. Although RequestFactory might be more elegant and extensible then its RPC counter part. The added complexity does not make it a better tool necessary.
My opinion is that the best architecture is to use two web apps , one client and one server. The server is a simple lightweight generic java webapp that uses the servlet.jar library. The client is GWT. You make RESTful request via GWT-RPC into the server side of the client web application. The server side of the client is just a pass though to apache http client which uses a persistant tunnel into the request handler you have running as a single servlet in your server servlet web application. The servlet web application should contain your database application layer (hibernate, cayenne, sql etc..) This allows you to fully divorce the database object models from the actual client providing a much more extensible and robust way to develop and unit test your application. Granted it requires a tad bit of initial setup time, but in the end allows you to create a dynamic request factory sitting outside of GWT. This allows you to leverage the best of both worlds. Not to mention being able to test and make changes to your server side without having to have the gwt client compiled or build.