Hi
The main reason was for simplifying dependencies, particularly with the new installers. The difference between the Tomcat bundles and the WAR bundles were minor (really, just that one had Tomcat in), plus making sure we were distributing a good copy of Tomcat that was not the same as the slightly customized one in the installers. It should be almost as easy as before - there's just the extra step as copying the contents of the webapps directory over your own Tomcat installation.
Those were the reasons - we're always open to suggestions to make as life as easy as possible for as many as possible!
Paul.