What I believe should be also discussed with m2Eclipse Team
is an ability of m2Eclispe plugin to ignore Scala compiler plugin if it is referenced from the pom.xml file:

<plugin>
				<groupId>org.scala-tools</groupId>
				<artifactId>maven-scala-plugin</artifactId>
				<version>2.15.0</version>
				<executions>
					<execution>
						<id>scala-compile-first</id>
						<phase>process-resources</phase>
						<goals>
							<goal>compile</goal>
						</goals>
					</execution>
					<execution>
						<id>scala-test-compile</id>
						<phase>process-test-resources</phase>
						<goals>
							<goal>testCompile</goal>
						</goals>
					</execution>
				</executions>
			</plugin>

Because what currently happens when both Scala and Maven Builders are active for a given project,
is Scala source compiled twice (which takes too long actually).

For Java source code, m2Eclispe has this hidden undocumented setting (in *.settings/org.maven.ide.eclipse.prefs*):

skipCompilerPlugin=true

I believe they should have something like that for maven-scala-plugin, too

Updating tickets (#3255, #3262, #3271, #3277, #3279, #3287, #3313, #3317, #3318, #3320, #3329, #1000000, #1000002, #1000004, #1000005, #1000007, #1000011, #1000013, #1000018, #1000019, #1000020, #1000022, #1000023, #1000024, #1000025, #1000026, #1000028, #1000031, #1000033, #1000034, #1000037, #1000039, #1000040, #1000041, #1000057, #1000058, #1000060, #1000061, #1000063, #1000064, #1000065, #1000067, #1000070, #1000073, #1000076, #1000080, #1000082, #1000083, #1000084, #1000085, #1000087, #1000088, #1000089, #1000090, #1000092, #1000093, #1000094, #1000095, #1000097, #1000102, #1000104, #1000106, #1000108, #1000110, #1000111, #1000116, #1000124, #1000126, #1000127, #1000129, #1000132, #1000133, #1000136, #1000139, #1000143, #1000144, #1000145, #1000148, #1000149, #1000152, #1000154, #1000155, #1000157, #1000158, #1000159, #1000161, #1000169, #1000170, #1000172, #1000174, #1000176, #1000178, #1000179, #1000183, #1000185, #1000188, #1000189, #1000192, #1000196, #1000198)

Some support is provided by the m2eclipse-scala extension to m2eclipse.