You *can* use webby in JavaEE Kepler, even if m2e-wtp is installed.
You need to tell m2e to use webby instead of m2e-wtp. You have 2 options :
- Either modify your pom.xml to add an m2e lifecycle mapping, like : 
	<modelVersion>4.0.0</modelVersion>
	<groupId>foo.bar</groupId>
	<artifactId>webapp</artifactId>
	<version>0.0.1-SNAPSHOT</version>
	<packaging>war</packaging>
	<build>
		<pluginManagement>
			<plugins>
				<plugin>
					<groupId>org.eclipse.m2e</groupId>
					<artifactId>lifecycle-mapping</artifactId>
					<version>1.0.0</version>
					<configuration>
						<lifecycleMappingMetadata>
							<pluginExecutions>
								<pluginExecution>
									<pluginExecutionFilter>
										<groupId>org.apache.maven.plugins</groupId>
										<artifactId>maven-war-plugin</artifactId>
										<versionRange>[2.0,)</versionRange>
										<goals>
											<goal>war</goal>
										</goals>
									</pluginExecutionFilter>
									<action>
										<configurator>
											<id>org.sonatype.m2e.webby.projectConfigurator</id>
										</configurator>
									</action>
								</pluginExecution>
							</pluginExecutions>
						</lifecycleMappingMetadata>
					</configuration>
				</plugin>
			</plugins>
		</pluginManagement>
	</build>
  </project>
 This will enable webby for this specific war project. Others would use the default m2e-wtp configurator.
- Or use a workspace wide lifecycle mapping configuration (all war projects will use webby). Open Preferences > Maven > Lifecycle Mapping > Open workspace lifecycle mapping metadata (you can change its default location), and add :
<lifecycleMappingMetadata>
	<pluginExecutions>
		<pluginExecution>
			<pluginExecutionFilter>
				<groupId>org.apache.maven.plugins</groupId>
				<artifactId>maven-war-plugin</artifactId>
				<versionRange>[2.0,)</versionRange>
				<goals>
					<goal>war</goal>
				</goals>
			</pluginExecutionFilter>
			<action>
				<configurator>
					<id>org.sonatype.m2e.webby.projectConfigurator</id>
				</configurator>
			</action>
		</pluginExecution>
	</pluginExecutions>
</lifecycleMappingMetadata>
save and reload the mapping metadata. You might need to trigger a full workspace build so that webby generates the target/m2e-webby/war folder.
Either one of these steps will allow you to do Run As > Run as webby on your project.
HIH
Fred