You've talked a lot about how TvTropes isn't suitable for literary analysis (the specifics elude me), but I haven't been able to parse your point, could you possibly elucidate on your thoughts of TvTropes as an institution?
The short version is that all systems of categorisation are at least in part prescriptive, in the sense that each one depends on a particular set of assertions about how the lines between categories ought to be drawn. When you sort things into buckets, you're not just describing those things – you're also enforcing those boundaries. This isn't inherently a bad thing, but it's critical to recognise that when you apply a paritcular system of categorisation to a particular topic, you're forcing that topic into a shape that will fit into that system's buckets.
To the topic at hand, then, the issue with TV Tropes is that its system of categorisation – that is, how it relates tropes into hierarchies, how it draws the lines that separate one trope from another, even its basic concept of what a "trope" is – are all informed by the fact that it started out as a Joss Whedon fansite, and even though most of its present users aren't aware of that fact, its analytic framework has never really moved beyond those roots. Any media that's understood through the lens of TV Tropes' system of categorisation unavoidably gets smooshed into the general shape of a TV show written by Joss Whedon, whether that was the intent or not. This is a perfectly fine analytic lens if what you're describing is, in fact, a TV show written by Joss Whedon, but it becomes a progressively worse fit the further you get from that sphere of competence.