[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.
Trying to figure out exactly what he means by individual parts of the story can be intentionally confusing and the stated goal of the work is intended to overwhelm on so many different fronts that it can be hard to hold a consistent view of what is the moral or intellectual message of the overall piece. Knowing a bit about Isayama though, clears up any ambiguity that might be present.