- the X packages come with menu items and they are maintained through updates
- most of the problems you describe seem related to RPM. The thing is noted for its database corruption, and once the DB goes, your box is toast. It is the very thing that drove me back to Debian (which was the first Linux distro I ever installed, so it *can't* be that hard!) after a tour of some other distros (Mandrake 6.* & 8.* and Suse 7.*)
For Java, I'm using the 1.4 SDK and/or JRE straight from Sun. It seems to have the fewest problems with the dreaded browser plugin. Park it in /usr/local and *link* jre/plugin/i386/ns610/libjavaplugin_oji.so to /usr/lib/mozilla/plugins. Works fine here.