I opened https://issues.jboss.org/browse/JBIDE-14720
Simple setup: Kepler RC2 package for Java EE, JBoss Tools from http://download.jboss.org/jbosstools/builds/development/4.1.0.Beta1b.core/2013-05-29_02-05-21-B272/all/jbosstools-build-sites.aggregate.site_41-Update-2013-05-29_02-05-21-B272.zip, wizard for "Java EE web project" for JBossAS 7.1, and finally NOT ANY PROJECT FACET is set.
I guess this is the cause of all the trouble, and should be fixed. When I try to set project facets manually, edit the pom.xml, insert DDs (web.xml, beans.xml, ...) then I'm running in the problem mentioned above.