[SPOILER ARLERT: Don't read this if you haven't read the scans and don't want to be spoiled]
I think we can start by saying Isayama is a nationalist and I've heard people say the way he draws Titans is somewhat anti-semitic.
The lesson of this serie also seems a bit reactionary, the fact that "walls work" for example, even if they end up not working so much in the end.
The genocide versus self annihilation aspect is also to be discussed I guess. On the subreddit, you can see many people that are pro Eren, pro destruction of the entire world. I guess if one thing can be said about this series is that there are really no actual good guys, everyone is a killer and all factions suck; whether that's good depiction of politics or not, I couldn't say.
I think you miss something calling it anti-semitic when the good guys are all clearly the victims of a nazi regime, right? The story really starts with Eren's dad in the ghetto, and those aren't exactly subtle about who the bad guys are (its the nazi soldiers that make people wear armbands). It runs into the same problem X Men does, where it accidentally justifies its racism but I think calling it anti semitic isnt the right way.