It’s been forever since Annie sealed herself within the crystal cocoon after her battle with Eren in the capital and outside of a flashback to the Battle of Trost we’ve not seen her since. As annoying as it has been with her effectivley removed from the story, I think there is a solid reason for it because I don't think Isayama has forgotten about her, as I've red some posts where some people think he has. After reading the latest capter, 91, I think I’ve figured out why Isayama hasn’t brought Annie back into the story yet, and what I hope happens when she does come back.
Annie, along with Reiner, Bertolt and Marcel (the one Ymir ate) were sent to the Walls in 845 and now it is 854 so if they received their abilities in 845 then Annie and Reiner will have 4 years left to live. However Marley’s plan to recruit Eldian warriors for their plans to destroy Paradis that we saw in Grisha’s memories in 832 called for children between 5 and 7. While obviously Zeke, who is 29 by 854, received his power much later, presumably because of he is a descendant of Ymir Fritz; it could still apply to Annie and Reiner. That means Annie who was 16 by 850 would have been recruited so between 839 and 841. If she hadn’t sealed herself away and escaped with Reiner and Zeke in 850 then by 854 she would be dead or close to it. I think that's why Marley is currently searching for a successor for the Armored Titan, because Reiner is going to die soon, and his power needs to be passed on. I think Annie sealing herself within the cocoon has physically stopped her aging so her 13 year “Curse of Ymir” has been halted, and will resume only when she awakens at a later point which means when she does she still has another 4 years left to live. I think Isayama is saving Annie for a later occasion where she needs to have a few more years left to live so we may not see her for another long while yet, but there is not a doubt in my mind that we won't ever see her again. I'm just really hoping it's not so someone can just eat her and inherit her power.
I’ve always found Annie’s character interesting because I don’t think she’s pure evil just a victim of Marley’s corruption. True she has killed several people, including Marco and Petra who were two of my favorites, but she also saved Connie and Jean, gave Eren combat advice, aided Marlowe and hesitated to kill Armin multiple times and she does appear to be somewhat remorseful of her past misdeeds. Armin even noted that Annie does appear to care for her fellow comrades more than she lets on. Annie also doesn’t strike me as being completely devoted to Marley’s cause like Reiner, but views it as a means to an end. Since she was presumably raised in the Liberio Internment Zone I think her father believes that her service to Marley is their way of being accepted into Marley as true citizens. I should also note that Annie initially didn't agree with her father's beliefs and even lashed out at him during a training session and crippled him, until she eventually accepted what her father was forcing upon her.
Eren now knows both from Grisha’s books and from memories of Grisha and Kruger what Marley is like especially for Eldian citizens and how most of them have been brainwashed into believing they’re the stain of the Earth, because of the actions of their “dreaded ancestor” Ymir Fritz. I think if Annie is told the truth and is promised amnesty in exchange for her assistace, she could be convinced to turn against Marley and aid the Survey Corps in their impending battle against Marley especially if it means getting back home which I think is all she really wants to do. There is also a possibility that she doesn’t know about the 13 year curse and if all she really wants to do is live, she may be outraged to learn that Marley has significantly reduced her lifespan enough to turn against them. Obviously the Survey Corps would all have their reservations about trusting Annie, especially Mikasa and Jean, I think characters like Armin and Levi who know what's at stake and what needs to be done would be willing to give her a chance. After all if she did betray them again it's not like Eren could't put her down if needed, and with Levi and Mikasa's help Annie would be outmatched.
The Survey Corps having Annie on their side could prove useful as they’d have someone who knows Marley firsthand and could have a potential spy within their enemies’ boarders, which could allow them to sneak in and destroy Marley from within. Plus Marley has access to 6 of the Titan shifters and while Armin now possesses the Colossal Titan the Survey Corps need as many shifters on their side as possible. And with Annie on their side they could identify all the enemy Titan shifters within Marley. Maybe she could help lure them out so their power can be taken by other Survey Corps members? I also think Annie may have feelings for Armin as she has been shown to respect him, and in the field had chances to kill Armin and didn't, which she later admitted she wasn't sure why she did. She also said that she was genuinely hurt that Armin used emotional blackmail to lure her into that trap, as Armin himself also admitted that despite suspecting her role in Sonny and Bean's deaths he didn't want to believe he was right and kept quiet. Maybe having a soft spot for Armin could be a motivating factor to reform.
I want Annie to come back as much as most people but I think there is a reason why she hasn't been in it and given the revelations in the more recent issues, I think this is why and what I hope happens when she does come back.