She obviously has to be a time traveler right? My first guess would be a new character Johns is building up or even a obscure one. But why not have fun coming up with guesses? Even if I have little hope of any of these being right.
Liri Lee? Last seen as the new Waverider/Linear Woman in Time Masters Vanishing Point. She has new powers we haven't seen explored too much. Plus in one timeline she became the Time Trapper, who usually sports a hood like this. Actually the Linear Men first appeared in hooded cloaks calling themselves the Brotherhood. Liri was known for being the one that bent the rules.
Lena Luther? Daughter of Lex Luthor, granted the first version is gone but she has connections to Brainiac and may be back in another form. As the big B has recently created a kid with Luthors' genes. Scott Lobdell has teased Superboy meeting his half-sister. Seems unlikely though.
Stephanie Brown! Bet you didn't see that one coming! She has taken the name of Spoiler to heart and goes to every book to find out what will happen to post the Spoilers online so she can ruin the relaunch. Superboy Prime helps her because he wants his own ongoing or at least a special when he beats up the Titans.
Bonnie Baxter? Yeah she was erased by Jason Goldstein BUT Flashpoint happened. If she's still a Time Master she'd want to right things.
Alex from the last Booster Gold arc. Many, including myself, thought she was the original woman on the JLI cover. She still exists in some form and knows time has changed. Raises questions but she's the only character that comes to mind that was directly related to Flashpoint.
Rani? Hey we never did know what her future was. And she was absent during Boosters' return to the Time Lab. Even if she's not an "official" Carter that family does like to sneak into crowds and provide easter eggs/break the fourth wall with the audience.