Refactor the code to share more code with mongodb and other ODM implementations. Can we extract stuff into common base classes or adjust mongo so we can extend from it? The current code is often copy-paste with some small edits all over which makes it hard to update with new features and bugfixes from mongodb.
Also have a look at the OXM - we probably could profit from collaboration there too, as PHPCR is somewhere between document store and XML database. http://www.doctrine-project.org/blog/doctrine-oxm-intro
Implement ObjectManager interface and maybe add to the common interfaces like findMany suitable for us.