[{"_id":ObjectId("5a6eb97b2937803b14255180"),"x":{"foo":42},"y":{}},{"_id":ObjectId("5a6eb97b2937803b14255181"),"x":{},"y":{"foo":24}}]

db.collection.aggregate([{"$set":{"sortKey":{"$ifNull":["$x.foo","$y.foo"]}}},{$sort:{sortKey:1}},{"$unset":"sortKey"}])