Ressurection Magic. Why the hell doesn't she use it more, specially on zero after he dies protecting her. I mean, originally the shinigami would go after the resurrected one and her, but at that point she was already pretty much in open war against the gods, just had killed the god of death, so there was no actual reason not to do it.
Probably because it was far beyond her power at the time—note that she immediately returns to her Himeko form, and though she changes back to Kurohime many times afterwards, she never has enough time to do it because she has another threat to deal with. Plus, who's to say that other gods wouldn't have noticed and come after her? In her state then, she would've been killed.
Notice when she used the resurrection spell on past!Zero. She is horrified because she knows that this always ends with the resurrected being killed for good. Also why she didn't resurrect Zero right after the fight with Darkray? Pure and simple, she was BSOD'ing at that point and couldn't think straight, much less shoot.
What is the White God Tree made of? I mean, the Black God Tree is made of angry ghosts but what about the White God Tree? Piety? Willing human sacrifice?
Well, it's more or less of the English publication company that bothers me (aka Viz Media). Why did they stop publishing the manga?
If Kurohime, Sword and Ouka fused together are strong enough to take out the goddess who created man, couldn't Kurohime, Sword, Ouka, Aika, Saika, Yukio, O-yuki, Yuuka and Kazuma be strong enough to combat Yashahime? And even then, they don't HAVE to kill her or Zero; they just have to free Yamatohime and supposedly the world's problems will solve themselves.
Why does Sword love Darkray so much? I mean, Yashahime's obsessed with him because she's fucked up. But excluding when she's tapping into her werewolf side, Sword's got a pretty good head on her shoulders. It also seemed that out of the Death Angel Squad, she's the only one who was in love with him. Will we ever find out why specifically?