I just started experimenting with the mongodb module and its fields storage module on a clean drupal install and it all seems to work fine. But what I noticed is that the content of the 2 custom content types is stored in the same collections (fields_current.node and fields_revision.node).
Wouldn't it make sense to have a separate collection for each content type? As queries are often per content type, it should reduce the scope of your query? Is there a possibility to do that with the current version of the module, or am I just not getting it?