Another TL;DR comment:
Something I touched on earlier: What will the default value for replicationFactor be when the collection is automatically built? One idea, but I'm far from saying it's the best idea, is to set the default to the number of servers in the cloud.
If the replica count is hard-coded to 2, or uses the number of servers, the following scenario would result either in no .system collection at all (failed create due to insufficient servers) or no redundancy: A user sets up a cloud, initially with one server, then creates a collection on that cloud to try things out before adding more servers and setting up their real collection(s).
I like the idea of not making the user do things manually, but if a user proceeds in the cautious manner I just described, I worry that we'll put that user in a bad situation at a later date when the server containing their .system collection dies. We can create good documentation, but unless the user thinks to LOOK for that documentation, they might get a nasty surprise one day.
Related: The reference guide probably needs a section describing problems that can arise from a lack of understanding, and how to remedy them. A possible section title: "Gotchas: Solving problems you may not know you have"