The Oracle
OKay, correct me if i'm wrong (as always), but i don't think the Oracle was the mother of the Matrix.
Okay, first of all, i have to make an assumption: The Oracle does care about what happens to the Humans and Neo, and will therefore try to help them in any way she can. Theoretically, this would mean that she tell Neo what she knows, including, we assume, that there were other anomalies. now, since she either didn't know, or knew and didn't tell Neo, i am going to assume she Doesn't know. This would mean that she didn't come into Existence until after Anomaly five had his code rewritten, aka gone to the source. Meaning that the Oracle is either killed or destroyed every reboot, and the Oracle could not be the mother, meaning it would have to be someone else entirely.
I know that i had to assume a bit, but it seems as if she truly wants to help Neo, doesn't it? Its a suggestion, reply so we can accept or reject this theory. Tell me if you think good idea or not.