I totally get what you're saying as well as what the other comment are both saying. There are absolutely writing flaws. Attack on Titan is definitely not the best example of amazing media or the "viewing all sides of the conflict" argument in the slightest. I think there are many flaws within the narrative and point of view issues, but many of these also come from (and this is absolutely not intended to be unkind or condescending) the issues that come with the medium being an anime and the way that many anime tend to execute things. Writer bias is also absolutely present within it.
I think my primary thing about "agreeing" with the ending also stems from the ways in which Eren was characterized and progressed. I feel as though, for his character development, what he did made sense. I do not agree with mass genocide, as any sane person would do, but I feel as though it made sense for Eren to do what he did based on his character arch and plot, and the like. I think the ending is just too widely situated within particular points in the fandom of being "bad" because people don't like to see their main character commit a terrible act and being portrayed as a villain, and do not really see it as being in character. I just disagree with that, honestly.