While I still disagree about Eren being a bad guy, I agree that there has to be one more twist.

Although I'm not even talking about a twist relating to Ymir or the bigger story, but more to what's going to happen. This is my hope more than my confident prediction, but I'd LOVE to see how Armin and Co. reach Eren, start fighting him, and even get close to finishing him off - when Mikasa at long las realizes that she was never under Eren's control and that she actually loves him for realz. We'll get a hilarious scene similar to Annie when she was exposed and weirdly blushing and all, this time with Mikasa "blooming" and even visually return to her more feminine look pre-timeskip. And then she'll defend Eren with all her might, because love trumps all.

As for overarching stroy twists, I can see 3 scenarios:

1.) Considering time travel shenanigans were introduced already, Eren might make his conscious travel back to his younger self and take over. Thus allowing him to do-over EVERYTHING. Basically playing a video game with a guide next to you. :>

2.) Eren finds out the hard way that Ymir wasn't the only god parasite-carrier and the world turns into a total war battlefield between different god parasite-carriers.

3.) Some other character finds the god parasite-source and intentionally gets one to be able to fight Ymir head on.

Or maybe the heroes fight Eren and the End.