It would be nice to be able to move 3D objects within the tree system. I can see how this may cause issues with synchronizing. But for items that are generated within Synchro this would be helpful.
You can now organize the 3D, Resource, Resource Group, and Task tables any way you want by right clicking in the table header and choosing Custom, then right click again to choose Group...
In the Group dialog, you can organize by any attribute you want (e.g. User Field)
I know this is an option, but with thousands of objects loaded, this is too much effort to organize. In our case, we have imported thousands of objects from links, but we are adding several items manually to clarify tasks in animations. Our preference would be to organize these items (leave our objects from links alone) so the tree doesn't become so cluttered.