Star, that's very helpful! It gives me some idea of how prevalent the exceptional children are. 3(or4)/59 and 2/52. So around every 20 - 25 babies as a loose guess. It may also be more prevalent when breeding a Master Parent as compared to a first time breeder or Trainee Parent. I know the software does change the outcomes of the villagers actions based on their skill status so part of the equation may have to do with the parents being Master Parents or not.
I'm so glad you've kept your genetic tree for your tribes! I got into this pretty much the same way as you, but with a twist. When I first began playing, there were certain villagers I simply thought were ugly so I altered them. Some of them I simply made changes to their face and/or hair. But some of them I completely replaced with a duplicate of my favorite villagers. Obviously, that really messed up the genetics. Here I was, thinking I had all these pretty villagers, but not really. When I decided to put the game back to the way it was originally written, all my pretty villagers were GONE and I was left with a bunch of brown and red heads!

Even worse, all of my blonde women were gone! I only had 2 blonde males left, and they were getting a bit old.
So that's when I began charting my villagers. I started keeping a spreadsheet on the parents and their children. I needed to have an identifier for each villager so numbering them seemed to be the most logical idea. And that's when it popped out at me. The children were the average of the parents, give or take 1-2 points. That explained why every villager gravitated towards the middle #15/#16 which are the brown and red heads.
I frantically wanted to get a blonde back! My favorite is the long blonde haired female, followed by the same female with slightly darker hair. I had lost every one of them. So I began finding the highest number male and female to breed. Anytime I got a child with an even higher number, I'd use that one as my new breeder once they turned 18. Slowly, I managed to get my blondes back! I got up to a 25, 26 and 27 female children with my original breeder pregnant again, hoping for a boy. If she has a girl and her current partner dies of old age (he's a #28), I have a good 20 years left on another partner that's a 27.
Once I got that far along, I decided to play with a second tribe. I paused the first tribe and started a new tribe which I named, "Vicki's Blondes". Only one problem. Not a single blonde in the original 7! In fact, most of the villagers are very dark haired! Ugh! I have no choice but to breed them as I needed to get the village established. And then I made a mistake. I allowed a #9 to ring the Gong. The Gong granted him wisdom. It was the first time it had granted wisdom so I didn't know what to look for. Then, that night, my #9 male breed with all of the females!

Turns out, the Gong made him a Master Parent.

It's not easy to get a tribe of blondes with a breeding-crazed #9 running around!
I've managed to stop him from breeding as much as he used to; although, he's still managed to get a couple more females pregnant. And then I've had two couples breed accidentally when I dropped one of them on top of the other, not meaning to (such as putting one on a hut to fix).
I've finally finished all the puzzles, got all my skill levels and have 30 or so Esteemed Elders. Only the first villager didn't make it to Esteemed Elder. All the rest have. That's a secondary goal of mine. All I have left are 3 bugs to collect, but with only 38 villagers (now 41 thanks to expectant twins and a singleton just bred). So I have lots of chances to breed any parents I want. The only problem is I really have very few parents I will even attempt to breed. My highest numbered parents in that tribe are #18s (a male and female). I'm breeding those two as fast as possible, but with just one couple and two "Isola years" for each child, it's going to take some time. My first child came out as a #18 female. I have a long way to go to get my beloved #26f.
I noticed you mentioned some issues with #9s. I have found some curious things with #9s, males only I think. It just seems they are different somehow. My rouge Master Parent #9 arrived unannounced (that I know of) and without any parents. He just ended up as a child in the tribe. I didn't really pay much attention to him until I realized he didn't have any parents showing even though he was under 18 and not one of the original 7. I've also ran into more exceptional children with #9s involved than any other number. It may be just a coincidence, but I'm not completely sure. So you got my attention when you mentioned issues with your #9.
I'm still not able to find a solid pattern to determining the exceptional children. They seem to be all over the board and not organized. But maybe I'm looking at it from the wrong angle. Maybe if I organized it around the children's numbers instead of the parents', a pattern may emerge. Since this is all in a spreadsheet, I just keep adding different possible equations for all of the exceptional children in hopes that I'll stumble onto a pattern. However, there may be other things at play that I cannot possibly account for, such as if the game takes into consideration whether the tribe is too homogeneous and needs a new villager to stir up the genetics.