So after diving into the subject of nested models/collections in Backbone.js and being very frustrated at how Backbone doesn't handle them, I eventually discovered a comment by Backbone.js creator, Jeremy Ashkenas on GitHub:
To reiterate, in brief -- Nested data objects are usually way less useful in JS than intelligently-organized "flat" data objects.
Flat models can be more easily manipulated relationally, and trivially loaded from and persisted to relational databases.
With nested models, you either reinvent querying into arbitrary JSON objects (like backbone-deep-model seems to do), or end up having to include something as large as JSONPath.
Flat models make it easy to serialize and persist atomic changes to the state of your app -- folks using deeply nested models often end up sending huge quantities of redundant data over the wire.
Basically -- we want to favor the normalized, relational approach to data modeling on the client side, over the "giant single global blob of deeply nested JSON" approach"
...these comments by Jeremy confused me so much when I first read them that I quickly realized I must be missing something very basic. It turns out I was right. Hopefully some of the answers I came up with might help someone else in their decision making process about how to implement their Backbone.js models.
"we want to favor the normalized, relational approach to data modeling on the client side, over the "giant single global blob of deeply nested JSON" approach
…what is not explicitly mentioned in that quote, but I believe important to understand (and which I did not previously understand), is that such an approach CAN be used with noSQL databases. That is to say that embedded/document-oriented schemas (e.g., that result in the 'single blob of nested JSON') are NOT the only schema one can use even with a noSQL context - a developer can instead create a flat schema by using references.
Basically, Backbone is very opinionated about a preference for the latter data modeling schema (e.g., referencial). This may be for a good reasons as @jashkenas says, but it also means that developers trying to use Backbone's normalized-opinionated modeling with their document-oriented schema (which is quite a few people it seems) are trying to make things fit together that were never really intended to. Which is to say that developers would probably do well to either switch all their data modeling to what Backbone is opinionated for, or else grab the right extension for the data modeling schema they do use.
As a final note, I believe the example Backbone.js documentation gives in regard to nested models/collections only exacerbates potential confusion, ultimately. On the one hand the docs say that Backbone doesn't support nesting, but on the other is an example demonstrating and mentioning...nesting? Similarly, StackOverflow is full of many examples of people figuring out how to cram their document-oriented data schemas into Backbone's reference-oriented architecture. It can work I guess, but eww.
Until recently I've been less than enthusiastic about Drupal 8, but I've changed my tune (and of course nothing is perfect; I am still a bit concerned/sad that Drupal 8 could possibly be leaving some smaller sites behind, but this is a ship that has likely sailed, so c'est la vie).
What led to this change of heart? Simply, my understanding of just how much, and in what ways, Drupal 7 and previous versions of Drupal differ from widely established/modern techniques and/or best practices of higher level computer science/programming. Arguing whether this is true is comparable to arguing whether square wheels work better than round ones. All of the best programmers, across many different languages, and frameworks don't end up at the same basic conclusions for no reason. This is empirically evident for anyone who has looked around, studied, and experimented with solving problems that, as it turns out, have already been solved before. Drupal 8 will stand on the shoulders of these giants of programming.
To wit, a Drupal 8 programmer will not need to feel behind the times to anyone developing in Java, Rails, Django, or you name it. In fact, a Drupal 8 programmer that embraces the changes and learns the fundamentals underneath the implementations will have a much easier time being able to grasp those other languages/frameworks because Drupal will share more fundamental paradigms with them than it differs by. The reverse is true as well, of course (e.g., programmers from other languages will have an easier time coming to Drupal).
So, to keep this short I'll just close with this - embrace Drupal 8 and the future by starting to learn all the design patterns and OOP fundamentals you can (I recommend not just reading, but making something medium to large sized from scratch). The truth is this; if you think it's time to ditch Drupal and reach for anything other than WordPress -- objects, interfaces, design patterns, dependency injection, event models, etc will more than likely still be waiting for you there (and if it isn't I'd recommend passing, anyway). Drupal's architecture is just catching up with the rest of the more advanced computing world. Hop on board.
P.S., the scale of refactoring that Drupal 8 is undergoing to shed it's imperative/procedural/tightly-coupled skin is truly a monumental task. Allocate your criticism and judgement appropriately, and give things some time to expand and evolve.
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I've happily reached a significant milestone in the development of my project, finishing a foundational layer that by itself could be valid to open source at some point.
Currently, I am using localStorage for my data store, and it's been working great for development purposes - it's basically a mock mongoDB for me (I'm storing nested objects in localStorage using a small jQuery library called jStorage). I'm purposely putting off the server side of this application because I want to be able to use the Symfony 2.3 LTS release, which is scheduled for May as middleware between the client-side and mongoDB. The temptation to use node.js is strong, and arguably would be the most performant option, but the reasons for picking Symfony are probably obvious to any Drupal developer.