Questions:

** Why does there are two maven_home's for root and system? as far as I know there should be only one maven_home we generally pointed by $M2_HOME variable.

It's only the m2 repository that will be different from user to user afaik. in this case there should two repos for system(portage) and root. It can be .m2_system, and .m2_root under /usr/share/maven-2.2, yeah? OR ideally, root .m2 should be located at /root/.m2/repository.

* replacing plexus-core with another name makes it work. But probably this isn't the correct approach since I see that "plexus.core" String is used when creating the ClassWorld instance in org.apache.maven.cli.compat.CompatibleMain. That class is the entry point mentioned in m2.conf file.
With another name, there's this error that I haven't tracked down yet. any clues? http://pastebin.com/zkbLqkyn

* and, why is there a separate plugins folder in maven_system_home?  It's set as "${JAVA_MAVEN_SYSTEM_HOME}/plugins" and JAVA_MAVEN_ROOT_PLUGINS="${JAVA_MAVEN_ROOT_HOME}/plugins"

Afaik, plugins are installed just like other jars. For example, maven-compile-plugin is at /home/kasun/.m2/repository/org/apache/maven/plugins/maven-compiler-plugin/2.0.2/maven-compiler-plugin-2.0.2.jar

* What's the reason to put maven-core at first. 01_maven-core.jar and 01_maven-settings.jar which are located under lib/ directory? The ideal path for M2_HOME is /usr/share/maven-${SLOT}!