i think a more simple explanation would be the fact that there have ones before, that each time a One shows up, he/she has to be dealt with accordingly, i'm sure the machines set up the whole keymaker/merv/door thing to make sure that only the One got back to the source. So each time one person believes so strongly that they can bend the rules of the computer world that it simply happens. Remember morpheus's speech in M1 about how the rules of a computer system can be bent even broken. Most of the rebels could bend rules all over the place, but only the One who believed in himself even more than the others, could break the rules, and of course once he began to do that he had to be stopped, thus the cycle. So I think that it is a random person, no one knows who it is, heck they weren't even sure if Neo was the one, he wasn't even sure! But he believed...
my theory about birth in the matrix...
as we all know, it takes nine months for a gestation period of a human being. i think that a pod grown human has none or minuscule amount of BTU's upon "sprouting" and it would take 9 months (this would be the amount of time spent in the endless fields) for a single pod grown human to generate BTU's that the machines could actually harvest. while this is happening, the machines pick a host in the matrix for the conception and introduction (birth) of said baby. the machine then introduce a "maternal" program into the host's brain for the RSI of the "mother" to change accordingly with time and the development of the baby.
when the baby is introduced to the matrix, his or her likeness is dependent upon the reactions of his or her parents. if they think the baby looks more like the father, the machine then programs the baby's RSI to look more like the father since the baby has really no conscious control over the projection of his or her RSI, the same works if they say he or she looks like the mother.
your thoughts...