Fractale/WMG

Phryne was raped in the past by
The leading theory behind Phryne's PTSD in Episode 7 after is that she was raped in the past, and the most likely candidate is ; even the dark figure from her vision morphs slightly and seems to resemble him. Alternatively, abuse could have been the contributing factor since
 * It steadily more likely through Moeran's off-hand comment that has sucked the life and love out of, Phryne mentioning that  has "defiled" them numerous times and her repeatedly referring to Nessa  as when she was "beautiful," and 's claim that Phryne and he have to tell Clain that they are

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.

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, 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.
 * That particular plot hole has more to do with the animators suddenly deciding to change the character designs. In the manga/novel art/whatever else the three stay with the same purple hair.

Fractale will have a sequel of some sort.
It makes sense, given the ending.
 * What part of the end exactly "makes sense" with regards to a sequel here? As far as I can tell Fractale can justify ending at this season because of the massive parallels between this and End of Evangelion. The two major plots were resolved - i.e. Clain's budding romance with Phryne and the Temple's attempt to reboot Fractale. Unless there was some outright declaration that something is to be continued in the last minute of credits, the Fractale anime can be considered a complete work for something with that much Mind Screw.

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.

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.