While the upgrade from Eclipse 3.6.2 to 3.7 went without nearly any trouble the upgrade of the Acceleo plugins to the versions provided with Eclipse Indigo was “a little bit more” problematic.
Starting the generator after the upgrade simply brought up:
Exception in thread "Main Thread" org.eclipse.acceleo.engine.AcceleoEvaluationException: The type of the first parameter of the main template named 'myTemplate' is a proxy.
The main template did not accept the model anymore. Although everything was registered and working with the previous version.
Googling a bit I found out that Acceleo provides a different serialization model which stores models in binary form instead of XMI. Since all my models I flipped the switch in the project settings: