These are what we call the 'YMMV items.' Things that some people find in this work. We call them 'your mileage might vary' because not everyone sees these things in the same way. This starts discussions in the trope lists, a thing we don't want. Please use the discussion page if you'd like to discuss any of these items.
With regards to Fumito, did he really love Saya despite ruining her life by brainwashing her, hiring people to play as her "friends" and having these people killed in a gruesome way? Or is he only obsessed with her blood and the Elder Bairns that he's willing to turn innocent people into them and eventually became one himself?
Yuka. She goes along with Fumito's plan where people got killed and yet, she eventually became the governor of Tokyo where she abolished the Youth Ordinance Bill which was implemented by Fumito in the first place. It's unclear whether she joins Fumito just to get what she wants and yet, she doesn't have any qualms for all the terrible things that he did.
There are also some who want to see a revenge-driven story but they ended up disappointed as most of scenes show more of the SIRRUT hackers.
Esoteric Happy Ending: Saya gets her revenge but what's the worth of it when she found out that the man who tormented her emotionally and psychologically, killed many people in the TV series and turned Mana's dad into an Elder Bairn happens to be obsessively in love with her and all that he did is for her own survival and to fulfill her desire to feed on humans which he already failed? And considering that one of the people who helped her get to Fumito happens to be in league with him all along, Saya would probably experience more trust issues and never touch a coffee mug again. She can't even go back to Mana after she found out that she killed her dad at the beginning of the movie. Her Walking the Earth at the end of the movie just shows that Saya would end up alone because she might not ever trust people again and end up hurting them if she does.
Fanon: Viewers speculated that Saya not returning to Mana after killing Fumito is her price for sword that she got from Watanuki earlier.
Foe Yay: Saya and Fumito which was started in TV series.
Watanuki only appears to provide Saya her sword. Then, he's never seen or mentioned again afterwards.
Yuka only appears in two scenes.
Rescued from the Scrappy Heap: Saya. After her incompetence and airheadedness in the TV series (though that was Fumito's fault), she proves herself to the viewers that she's definitely badass and saves a life.
They Wasted a Perfectly Good Character: Asides from Mana and Kuroto, the rest of the SIRRUT members don't have much background which makes you doubt about being resistance fighters against an organization with a private army and the capability of creating and controlling human-eating monsters. This goes the same with Yuka who only appears in two scenes and yet, it would have been interesting on what kind of role she contributed to Fumito's organization and possibly, her interaction with Saya if only these two ever meet again.
They Wasted a Perfectly Good Plot: The movie may have become better if they show more of Fumito's side, particularly his motives and his obsession with Saya. Or how the Youth Ordinance Bill was used in the movie, which was hinted that it's used to cover Fumito's activities. Or what would be Saya's reaction if she meets Yuka, her "supposed friend". Or how Fumito and Saya first met before the events of TV series. Or anything related to Saya's origins or her adventures before meeting Fumito.