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Project properties->Project Facets->Modify
The WTP project wizard doesn't save the facet version you have chosen and there isn't any UI to set the deafult version for a facet.
However, you can create a user preset (configuration) by clicking the Modify button on the first page of the WTP project wizard and save it with "Save As".
You would need to create a new preset for each type of your project (Web, EJB ...).
Got it. Thank you!