Preferred is overloaded. Many use eclipse, a few still use Intellij. I was a long time Intellij user who has switch to eclipse when we moved jbossas to svn as Intellij was broken for svn.
I do see this issue with getting the eclipse workspace in synch with the build and thirdparty contents when a workspace is first setup. The best approach I have found is to checkout the project from the command and build it to create the thirdparty contents, and then import this into the workspace to pickup the projects. Subsequent updates to thirdparty may require cleaning the workspace. Selecting all projects and refreshing them, followed by cleaning the workspace has been working for me.