I believe that part of the reason that stories can be written badly and get popular or are made popular anyway is the lack of literacy and critical thinking skills.
But it also has to do with changes in fandom and audience expectations over the years. When a certain dynamic gets popular, other creators look for that dynamic or recreate it themselves (hence the gradual development and use of literary tropes).
When you look at how the narrative treats Ilya versus Shane, or at least when I do, what I also see are narratives that came before them that are the exact same dynamic.
PARTNER A: This one is not to be criticized and all of their trauma/troubled past explains/justifies all of their crappy behavior and if you disagree with that, you're in the wrong. This partner can do whatever they want and act however they need to in order to prove that they are the better partner in this relationship, even if the actual dialogue and behaviors shown prove that that just isn't true. This is almost always the writers' favorite character, and it's definitely most of the fandom's favorite character.
PARTNER B: And over here with the other partner, what you see is the suggestion that anything bad that happens to them is their own fault. They deserve it. They deserve their trauma. If their partner treats them horribly, they deserved it. If they stand up for themselves, they are selfish. They are usually mocked or made fun of or even destroyed by the narrative. If they want something to be just theirs and they don't want to give that up, they are punished narratively. Other characters are written in ways that push the narrative, even if you can prove through the text/context that it just isn't true.
The relationship doesn't even have to be Canon for this to happen. Some of the most popular ships have this same dynamic even if they never become Canon.
For most heterosexual relationships, A is almost always the male lead and B is the female lead. (A good Het example of this might be Dawson and Joey from Dawson's Creek).
Fandom examples (using TV/Book Source only) *mostly queer because that's just about all I watch or read about and as I stated the Het examples are usually the Male Lead and Female Lead*
Also I'm sure there are other examples from fandoms I have not been a part of, but since I haven't been a part of them, they aren't included here for obvious reasons.
Canon and Non-Canon (meaning romantically) Relationships:
KLAINE (Glee) - A is Blaine Anderson. B is Kurt Hummel.
A minor Het example for Glee that actually goes against the usual Het trend is - A is Rachel Berry. B is Anybody She Dates).
MALEX (Roswell, NM) - A is Michael Guerin. B is Alex Manes.
(Older show) BRITON (US version of QAF) - A is Brian Kinney. B is Justin Taylor. (Case of a milder example of the trend because Brian has a lot of "haters (deserved)" in the fandom).
MALEC (Shadowhunters) - A is Alec Lightwood. B is Magnus Bane. (Trend is more obvious in the books).
CALZONA (Grey's Anatomy) - (multiple queer and het examples but the most glaring queer one is this one) - A is Arizona Robbins. B is Callie Torres.
(Older show) JANTO (Torchwood) - A is Jack Harkness. B is Ianto Jones. (Also a milder example of the pattern simply because they didn't get enough screen time for it to be more obvious).
PATRICK/DAVID (Schitt's Creek) - very very mild example because this is the best written show out of all of them and the pairing is the most equal of the examples - A is Patrick Brewer. B is David Rose.
SCILES (Teen Wolf) - completely fanon obviously but this also goes for their canon friendship - A is Scott McCall. B is Stiles Stilinski. (Another rarity in this pairing is that Stiles is usually favored over Scott in fandom and this isn't the biggest ship for Stiles).
BUDDIE (911) - A is Eddie Diaz. B is Evan Buckley.
(Older show) BO/LAUREN (Lost Girl) - A is Bo. B is Lauren.
(Older show) SHANE (L Word) - Shane is just an A. Regardless of the pairing she is in.
HOLLANOV (Heated Rivalry) - A is Ilya Rozanov. B is Shane Hollander.
Why I pay attention to this is because PARTNER B is almost always my favorite character out of the pairing (and in most cases my favorite of the show). And that is true for every example I mentioned.
These patterns continue because they drive the fandom responses. Comparisons to toxic Het ships are valid comparisons. One queer character gets treated like the sole male lead and the other gets treated like the sole female lead.
One "can do no wrong" and the other "can't do anything right."
This pattern is never going to change unless this dynamic is talked about. Yes, it's "just" fiction. But fiction is important because it's a reflection of culture changes/dynamics.
It is important to look at these relationships critically BECAUSE they are popular.
Ilya and Shane aren't always toxic in the narrative. But it is important to show how they changed and grew as a couple. It is also important to be critical of the narrative if only one of them gets a true HEA and the other just gets the HEA "leftovers."