Just throwing something out here.
Since Ritsuko's mother had dark red/purplish hair, and Ritsuko's natural hair is that same color, maybe Mari is a kind of long lost modified clone of Naoko. Sort of like Rei is of Yui. Lets say Ritsuko wanted to bring back her mom and abandoned the project, then SEELE found it modified her experiment for their needs, then picked up where she left off. Maybe the Moon Giant turns out to be a third seed, as well as the mysterious third Angel, and Mari contains part of its soul. Either that or she just has a normal human soul.
Seize the day.....by the throat....
I hate mcdonalds because their mascot is a creepy spooky clown who looks like he smells funny. Seriously every time I see ronald I think he's secretly some sort of rapist who turns people into hamburgers. Also their food sucks. -Defectron
Our plumbing is messed up and my dad will not call anybody because he's a cheap asshole. Fuck you old man, fucking call someone. Some of us want to stay sanitary. -backseatjesus