spot on. MongoDB is a step backwards in abstraction. The RDBMS geeks had this figured out in the 70s. Hence the "relational MODEL" vs "document STORE" transparent step backwards in generalization.
MongoDB is just locking you into a specific materialization of an ill-specified data structure. PostgreSQL's team hacked out JSON support in about a year or so, since they are working at a higher level of abstraction and could insert the "MongoDB model" at the proper place in their system. Now if you really need to store "documents" in your database and query lazily-defined fields you can do that for those edge cases (and lets face it, those are edge cases) and use proper relational modeling for the rest of your model.
Document stores are supposedly "more agile", but by conflating queries, the logical model and the physical structure, they are actually less agile. You've mixed the three things together and ossified around a single model of the domain. When the required view or model changes, you have to write workarounds.