Yep, i’ve build my own archetype and everytime i’ve created a new maven project with this archetype the java nature has been missing. So i’ve searched for more then 8 hours for a solution and finally found a small page of a developer who had the same problem. The solution is so easy … just delete the .metadata directory of your Eclipse Workspace and every Maven Project with your archetype will have the java nature in that Workspace out of the box.

Hope this helps