Whether the writing was garbage or not isn't relevant to be honest - because controversy was spun by people who only knew the game's story through hearsay of the leaks before the game even came out, and majorly it was to do with accusations of "wokeness" and other brainrot - so yes clearly it was an issue, of course it was an issue.
It wasn't really the substance of the game that the usual outrage grifters latched onto so it's not relevant to the discussion of the controversy.
As for more women being protagonists - sure, idk how you can say that so confidently, I suppose you have a convenient framing for what counts as "big games" to support your point, but I think the quantity was never really an issue.
Honestly more men being protags in games is okay, what I take issue with is that whenever something interesting happens, like oh I dunno, a game makes a woman kinda buff and mean looking, people bitch about it like no tomorrow.
So of course it's an issue. It always has been.
In 2013-ish, Anita Sarkessian made some exceedingly light feminist critiques of video games in and it was an issue.
In 2014-ish, A woman made an indie game that's honestly really good even to this day (Depression Quest) and it was an issue.
In 2020, a game came out where a fictional character (Abby) had muscles and it was an issue.
Nowadays I guess the most famous example would be the "FUCKING GENDER AMBIGUITY" screaming guy who didn't like Starfield's pronoun selection screen or some such.
Then people went truly psychotic in a deranged hate campaign against some random inclusivity consultancy Sweet Baby Inc. over games they were reportedly never involved with because there was women, or something, somewhere.
Hopefully you get the idea.
It was precisely the issue that a woman was the main character in a video game but was not in fact "Metroid from Metroid 1986" but a buff, angry, unattractive, hateful and morally grey character who does shitty things, sorta like Joel - in other words - she was something a lot more like a real person in a mature story, not a single digit frame twist from 40 years ago that amounts to an Easter egg turned geek culture cringe factoid parroted by the kinds of people who wouldn't understand RLM's "Nerd Crew" show is satire.
You can see some of the worst examples here, cherry-picked as they are, juxtaposed with what actual critique is: https://www.youtube.com/watch?v=dVQcZa4O01A
You can also visit the steam store page and look at the negative reviews, or peruse the cesspit subreddit /r/TheLastOfUs2 posts the time of the game's leaks and release to see people bitching about everything from pride flags in Seattle(!) to Abby being made too likeable to accusations of this or that character being le ebil transgender or whatever else that sounds like it came out of a /pol/-themed magic 8 ball.
Hell, there are utterly deranged people in the steam reviews for this game now bitching about the show - about the actress that plays Ellie and one guy even implies she is "down syndrome representation".
Like, what the actual fuck?
As for the game, the game is ok, I'm playing it right now, it's less boring than the first so I like it a lot more, the AI actually lives up to the bullshit promised in the first game's trailer, but it's too long and yeah the writing is too on the nose sometimes, though I do like the characters and the atmosphere a lot. Idk if I "love" it, but I do find it way more fun as a game and far more interesting from a story perspective.
What it definitely is though is controversial as fuck and that's just reality. People made a whole subreddit just to hate on the game that's active to this day and most of their issues aren't even to do with the game - they even pretend to hate the TV show they haven't seen too.
