Ever since Hououmaru was introduced, she's done next to nothing. Despite being a named character, and being fairly prominently shown whenever Ragyo's around. She's stood around in the background and been given zero backstory whatsoever. And then, in the post-credits scene at the end of this week's episode, she voluntarily allows herself to be absorbed into Shinra-Koketsu. For what reason? We're never told. We don't know what effect her being absorbed has, and we don't know what her motivation was to allow it. Also, Ragyo is almost certainly pretty much invincible in Shinra-Koketsu. It wouldn't be much of a final episode if she weren't, really. And the heroes are all out of final trump cards (at least as far as we know, though it seems likely). So if Ragyo can't be killed from the outside, then she's almost certainly going to be killed from the inside. Hououmaru's going to either kill her and take over Shinra-Koketsu, or something similar, and reveal her reasons for doing so (my prediction is the good ol' "this world sucks and needs to be destroyed because I had a tragic past" trope).
There's a Simpsons scene that kinda describes what I'm thinking, weirdly enough. It's the episode where Fat Tony's mob squares off against the yakuza at the end. And through the fight, there's this short yakuza in a white suit who just stands there doing nothing. And as Marge makes Homer stop watching the fight and go inside, he protests by saying (and I'm paraphrasing here) "Aww, but Marge, the little guy in the white suit is gonna do something cool, I just know it". Then as soon as Homer goes inside, you hear the white suited guy let out a yell as he kicks a few mobsters through the Simpsons' window. It's kinda like that. Hououmaru's been standing around in the background doing nothing for far too long for her to just be a random background character with no story. KLK has been full of twists, in fact the latter half of the show has been almost nothing BUT twists. And Hououmaru being the true final boss would be both the ultimate twist, and continue Imaishi's legacy of Gainax-trolling (Panty & Stocking, anyone?).
And as Midonin pointed out while I was writing this entirely-too-long theory, her name DOES have phoenix in it.