I try not to obsess over tropes. If a story is well executed and I lose myself in it then I'll forgive pretty much anything. If you can't suspend belief or find yourself captivated by the protagonist's struggle then no amount of subversion will do anything.
Tropes can be a reason we watch a genre. If there are too many elements outside genre conventions it can sometimes turn us away.
We go into a magic trick knowing the magician is going to guess the card, but how they get there and the show they put on is what keeps our attention. That's why I love Columbo. You know who the killer is, the interest is on watching Columbo figure it out. You don't mind that he says "Er, just one more thing" in every episode because you're so invested in the cat and mouse that the whole plot builds to that Columbo moment. Columbo's "why dunnit" or "how-catch'em" tropes can be viewed as a deconstruction of the "who-dunnit" trope, but they are still tropes of their own.
Thinking too hard on the nuts and bolts of story has limited use. imho. Tropes become tropes, often because they work structurally or they act as shorthand for some element or character that does not need the rich, detailed inner-life and backstory of out main protagonist.
A friend of mine, some years back complained about why women were often overtly-feminised in comics, and a comic artist friend replied because these costumes and body proportions are a short-hand for character traits (e.g. gender) within a highly stylised medium that suit the reading flow of a comic page.
Comic artist's control the pace of a story using the form constraints of the medium (number of panels, amount of words of dialogue, expanded action, the gutter etc) and, sometimes, being able to discern a character at a quick glance aids intelligibility in fast paced scenes.
The same thing goes for character - the Harry Potter orphan trope exists to quickly gain reader sympathy. We might view that as manipulative, but telling a story IS manipulation, in a way - you're being manipulated to put yourself in the main character's mind and sympathise (or whatever the intended emotion might be) with their plight. Cultural knowledge helps produce a vivid image, more readily than the unfamiliar.
When we say - oh I hate in when so and so is a Mary Sue or Gary Stew, we might think we're railing at the trope but we probably have several other characters that you can make a similar argument for that are personal favourites. What we're reacting to is the way the character is executed...
Reducing any fiction to a set of tropes is reductive and all stories will at some point begin to look the same if you zoom far enough out.
Part of me rebels against the idea of thinking analytically about story, thinking creativity should "come from the heart", but the editorial part does appreciate that absorbing the technique infuses the heart with greater range.
There are probably elements that annoy certain groups of people - like physicists who get annoyed at the sound of engines in space -- but I don't mind dramatic license. It doesn't matter to me if the physics of a story don't match reality, so long as they're self consistent and there's plenty of juicy human drama.
