It is being discussed at this bugzilla post:

https://bugs.eclipse.org/bugs/show_bug.cgi?id=213780

Another thing I've learnt: The initial poster here mentioned that he was hoping that the "General > Compare/Path > Initially show ancestor pane" setting should have allowed it to be one way or the other, but after I read further about this setting, that doesn't appear to be its purpose:

http://help.eclipse.org/helios/topic/org.eclipse.platform.doc.user/tasks/tasks-68b.htm

On this site, it gets described as:

• "Initially show ancestor pane"
  
  Sometimes you may want to compare two versions of a resource with the previous version from which they were both derived. This is called their common ancestor, and it appears in its own comparison pane during a three way comparison.
  
  Default: Off

So it seems this is more related to three-way comparisons rather than a control for whether to display old-vs-new or new-vs-old.

MercurialEclipse, on the other hand, always puts the newer version on the left.

Note that the local-on-the-left approach is consistent with the directions of the arrows in the synchronize view, where CVS and MercurialEclipse both badge outgoing changes with a left-to-right arrow, and incoming with a right-to-left.