In Eclipse, everything is a plugin, including the IDE itself. So, if there's something which bothers you, all you need to do is replace the plugin with something which works in a way more consistent with your personal preferences, or if the plugin is open source, tweak the existing plugin to suit your needs.
In my case, what bothered me was this: I don't have any reason to look at .svn-base files or .class files, so I'd prefer they not show up. Playing with working sets doesn't solve the problem, because (as far as I know) there's no way to exclude .svn folders from the working set without adding all the files individually. I tried to add extension points, but I could never get the filters to show up. So, all other options exhausted, I went looking for a way to modify the source code.
In order to modify the "Open Resource" dialog, I needed to find the FilteredResourceSelectionDialog class found in the org.eclipse.ui.dialogs package in the org.eclipse.ui.ide Java archive. A bandwidth-intensive way to get the source code for that one source file was to download Eclipse Classic, and find it in the src.zip found under org.eclipse.ui.ide in the org.eclipse.platform.source folder.
I then overrode the matches method in FilteredResourceSelectionDialog.ResourceFilter to exclude all file names ending in .svn-base and .class, created a quick build file to include all the Eclipse plugins jars in my classpath, compiled, copied the resulting class files into the appropriate Java archive, and got this: a clean view showing only the files I might want to open.