Phryne was raped in the past by Barrot.The leading theory behind Phryne's PTSD in Episode 7 after Gail's attempted to rape her is that she was raped in the past, and the most likely candidate is Barrot; even the dark figure from her vision morphs slightly and seems to resemble him. Alternatively, abuse could have been the contributing factor since Barrot was pretty determined to check if Phryne was still a virgin, which would eliminate the rape theory.
Fractale will have a Bittersweet Ending.The Fractale System will either become restored or will collapse, and not everyone will be pleased with either outcome. And if Phryne and Nessa do unite as one to become the "key," they may not retain their personalities or bodies, possibly leading Clain to choose which girl he wants be with or one of the girls might pull a I Want My Beloved to Be Happy and sacrifice herself.
An anime character's hair changes another color of the rainbow with age.Once it's revealed that Nessa, Phryne, and the Arch Priestess are all clones of Phryne, when you consider their ages, their hair will start out as red, and then slowly fade into purple. This could possibly be said for a number of other anime characters in other shows, even though we never see them in different ages, and are never mentioned.
Fractale will have a sequel of some sort.It makes sense, given the ending.
Barrot's treatment of Phryne is meant to echo otaku attitudes toward "2D girls."Misplaced parental affection has been theorized as one of the roots of moe (e.g., by Ken Akamatsu), even though sexual attraction often comes into it as well. The disproportionate value placed on her virginity mirrors the infamous incident when the female lead of Kannagi (the anime adaptation of which shares a director with Fractale) turned out to have an ex-boyfriend and readers were reportedly outraged. Otaku hold a desire to possess and believe it to be "pure love;" Barrot represents the logical conclusion of that mindset.
"Phryne" was completely destroyed in the end.Nessa is regularly called the "mind" of the two. When they are joined, Phryne's psyche is completely eradicated and replaced by Nessa. Thus, it was Nessa claiming her love for Clain in the end.