The Princess 99/WMG
Crafters du sang/The Blood Shamans are Vampires
It makes sense when you consider that Crafters du sang are unliked by other Crafters and they apparently need to spill blood in order to use magic. It might also explain why they were imprisoned in Eaudazo.
Skye is a Crafter from our modern world or from the not so distant future
Skye makes constant references to the modern world, like TV, movies, and the internet. Guessing from the slang she uses, she's most likely from twenty or so years into our future. Wilde mentioned that the Craft is always changing with every generation, so Skye's powers could be a result from a new generation of Crafters having different ablities.
Skye is a God
Skye abilities range from regular magic to being able to literally yank demons out of people and it's made obvious to us that she is beyond human and might be made out of energy. Most likely, Skye is some kind of goddess or immortal being.
Flow isn't a student at Edgewood
Well, not officially at least. We know that Flow is working undercover as a member of Lion & Unicorn and we often see him talking with Prof. Sweet. Other than that, we never see him in class or hear him mention about assignments or homework except for casually. He might be posing as a student and having someone else do all the work so that he can go about "more important matters".
Wilde is Axel's biological mother
We already know that Birds of Prey manipulated Axel's memories to think she was just a normal farmer girl and that destroying the music box fixed all of Axel's memories but we're never exactly told how far. Wilde tells Axel that she was abandoned but she could have been saying this to put distance between them. Bird of Prey mentioned how they had used other children before as assassins, and it's not unlikely that Wilde would use her own child as a guinea pig.
Eulalie is Brig's sister
This rumor is actually mentioned at the very end of the book. Whether it's true or not is debatable. Brig and Eulalie both mention that they are cousins, but Eulalie seems to share many of Pai's traits - kindness toward strangers and empathy. Eulalie's empathy may be just as extreme as Pai's, which is why she is a space cadet. Her empathy may be interfering with her ability to think.
Skye is Satan
Think about it: Skye complains about being tossed out of her home by a "hexa-bastard" whom she does not name. It's vaguely hinted at why or how she got removed from her home, but it seems to have been a fight. The "hexa-bastard" in question, was probably a higher power and is always referred to as a "he". She tempts, teases, and dresses rather scantily. She is powerful but is too lazy to use her more-omnipotent abilties. She even commits crimes such as counterfeiting moneye and avoids helping anyone but herself, save for the last few chapters of the book where she does a Face Heel Turn and helps Axel. Other than that, she's selfish. Sounding familiar?