Outside of the terrible worldbuilding in the latter part of the series, and blatantly ignoring elephants in the room like Levi's constant fucking up, and Eren's psychotic behavior like you mentioned, AoT's biggest problem is its lack of commitment.
Yeah, its really AoT's wish-washy nature that defines it. It couldn't stick to horror, it couldn't stick to shitty WWI-WWII analogue, it couldn't stick to time travel, it couldn't stick to supernatural, it couldn't stick to fucking anything.
AoT had no idea what it wanted to be and plot points were just driven by what Isayama wanted to write that particular month. Everything is basically author fiat, and I think that's where a lot of the problems of the series comes from. Its why shit just turns on a dime without any rhyme or reason. Nothing really makes any sense.
Even the ending, which was fucking hysterical and NOT what Isayama had intended (Don't believe that, he's full of shit. He had every intention of making Eren genocide the world and kill his friends). I mean, you only have to look at the last sections to see how much Eren is winning for him to just randomly fucking lose out of nowhere.
The problem is that its VERY clear that Isayama and/or his editors realized what sort of message a genocidal idiot winning would send, so at the (literal) very last second they turned around and basically author fiat make him lose. Don't get me wrong, I didn't WANT Eren to win, its just that the way it was written there wasn't any way he could lose. And in basically the last few chapters its a major reversal, yet again, from the direction the manga was going in.
People like to say ANYONE CAN DIE ITS SO HARDCORE, but that's honestly only true before the basement. Sasha dies because Isayama fucking hated her and wanted her dead, and Hanji bit the dust because he fucking HAD to kill off a character during the end. Other than that, shit stays pretty static.
The thing is its such a great horror idea, they basically go "And then we killed all the titans by luring them to the gate and smashing their heads with a log." Its a joke. AoT is a textbook example of how not to write something. I mean, the last leg of AoT entertained the fuck out of me because the entire final arc was just the manga ripping its own guts out. I've never seen a story suicide itself in a more hilarious manner. I mean, I think it basically blew its brains out when it insinuated Eren had a detailed plan and instead it was just revealed his plan was 'lol kill everyone'. I thought that was the dumbest fucking thing. You really didn't need to hide that plan for five fucking years or whatever. Nor is it an 'amazing' twist because its the fucking most obvious plan out there.
God, this manga is so fucking braindead its hysterical.