Social issues definitely seem like part of it now, but Kotaku was disliked in hardcore communities well before Gamergate or any of that other nonsense. My recollections of late-2000s Kotaku are similar to how I feel today about a lot of tech publications where personal expertise in their subject area makes it painfully obvious that they don't really know what they're talking about.
When you spend hundreds to thousands of hours mastering a game and immersing yourself in the culture surrounding it, an article on "your" game, unless it's written by someone as keyed-in to the meta as you are, is likely to come off as a series of poorly informed hot takes. In other words, generalist journalists frequently have a hard time developing the level of experience in a particular area necessary to write about it in such a way that's not laughable to the "experts". This effect is particularly bad in video games, where the amount of rabbit holes you can pour yourself into is practically uncountable. Everyone's an expert on something, and it only takes one crappy article on your pet game to destroy your confidence in anything that outlet produces, even if you lack the experience to see the lie in each and every piece.