After some discussion with a colleague from another company that also uses App Engine, he told me that he managed to cut down his app warm up time from ~15 seconds to ~5 seconds
One way this can be achieved if by doing the deployment through Ant, as described in: https://developers.google.com/appengine/docs/java/tools/ant
Next you can modify the ant build.xml file to call the ant command for building the jar file. Just before the actual deployment you can either delete or move the compiled artifacts away. The build jar-file should be placed in the WAR/WEB-INF/lib folder.
Drawback of this solution is that you have to deploy through the build.xml, i.s.o. through the appengine eclipse plugin.