The Hibernate Tools plugin will not install on a Gentoo emerged version of eclipse-sdk. If you compile eclipse-sdk with Java <1.5, a few internal eclipse plugins are not compiled, including org.eclipse.jdt.apt.core, which is a dependency of Hibernate Tools. Therefore, we need to compile Eclipse with Java 1.5 I'm working on making this possible now... but I have no idea how hard it will be. I really need Hibernate Tools, as you may be able to tell :-)
In reality, eclipse actually DOES require 1.4 to compile. It requires 1.4 for some plugins, and 1.5 for others. If there are some plugins not being built though, that's another issue...
Need to know things like, what version of eclipse you are trying this with.