The entire manga is the result of Katou's dying acid trip.Think about it. Katou invents Setsuna and Sara as a means to cope with his own problems with Brother-Sister Incest and creates Uriel as a surrogate father figure to replace his real one. Katou's memory problems occasionally seem to correspond with the manga getting crackier than normal, plus, things wrap themselves up (comparatively) neatly just two volumes after Katou gets Killed Off for Real.
Kira meant for Setsuna to become Alexiel.His decision to put Setsuna's spirit in Alexiel's body was premeditated during the ten or so chapters he spent staring at her corpse in the crystal. Kira assumed if Alexiel's original spirit and her body were reunited, Setsuna's consciousness would disappear and Alexiel would reemerge. The fact that he was wrong, more than anything, accounts for his depression during the rest of the manga.
Kato is actually the reincarnation of Lucifel's best friend who committed suicide after Lucifel humiiated him.
The embryo used as false evidence during Sara's trial is actually Raphael's.
Sara and Setsuna will eventually have a childand it will be Kato's reincarnation
Alexiel wasn't an angel after all, but a Shinigami.And Kira was, in fact, her Zanpakuto spirit. She just was thrown into a different dimension, or a Lotus-Eater Machine; she could even be the Soul Society King as well. What, it makes a bit more sense than the several Instrumentality and Time Lord theories you see out there!