I really didn't get the vibe that there's some kind of pandering going on with Zero Dawn (haven't played the sequel). I would also note that it's extremely common for video game characters to be Mary Sues, probably because they're often a stand-in for the player. In this regard, Aloy is not particularly different than a Gordon Freeman or a Link. Perhaps that's an indictment of how poor the writing in Zero Dawn is, but it's not unusual.
The character writing in Forbidden West is largely of the same quality as Zero Dawn: serviceable with a few outstanding characters (none of whom are the MC, unfortunately).
I feel like the reason it’s suddenly become an issue is that the quality of the Main Story took quite a drop in the sequel and it’s easier for people to pick out and criticize examples of poor characterization.
And to be fair, I never thought Forbidden West would be able to match/exceed the fantastic Zero Dawn plot - since ZD relied on a fantastic sci-fi premise that couldn’t be easily repeated once the “truth” had been revealed. But going with cackling immortal demigods dressed like a low budget episode of Star Trek: TOS was a poor choice for the middle act of a trilogy.
What’s really strange is how the new FW expansion lays out more breadcrumbs for the closing act of the trilogy that honestly should have been part of the second act (eg: VAST SILVER and the interactions between Old World AIs). I’d be less disappointed in the mustache twirling, scene eating, villains in sparkly spandex if they were the final remnants of humanity’s ancient hubris that had to be dealt with to bring lasting peace.
