Agreed, it is not inherently flawed for sure. Like I said before, there are games I've enjoyed with queer characters. I mentioned a few of them. Dragon Age: Origins, Mass Effect, Witcher, etc... but those characters were characters first and their sexuality was second. It seems like in some modern games you are supposed to like characters without knowing much about them aside from their sexuality or minority status and that is simply not effective writing for a lot of people.
Personally, I find it off-putting when people make sexuality their personality and it has nothing to do with gay or straight. Like the guy whos like all macho and talks constantly about how many women they sleep with. The same for the gay person who things who they sleep with is the only important thing about them. That's not a characteristic that would make a character likeable in my opinion, but modern games want you to like personalities like these.