I was being a weirdo and attempting to predict the gen 5 pairings (some were pretty easy to see the line... but omg trying to draw lines for most are hard and trying to figure out locations on the Unova map are gonna drive me insane I pity you) and came across an idea for a side scene.
Undella town is Cynthia's summer vacation destination so perhaps after getting pregnant by you, she goes to Undella to get away from public attention only to bump into you again ... and ask for seconds ;). Perhaps its only available if you got Arceus, breed Cynthia and then breed Caitlin.
Frankly, Undella town seems like a breeding ground (tee-hee) of potential side scenes since you can literarily bump into the Unova female gym leaders and elite four in Undella town and specifically the female ones. A bikini party of baby mommas imagine that.
Also things that seem possible but also try-hard would be to change dialogue like Caitlin would point out seeing Cynthia pregnant before you even do her breed scene like with Karen and other changes associated with the Karen-Agatha stuff, perhaps changing Cynthia's second ship text depending on if you did the side scene or not like perhaps she is disappointed if you didn't do the side scene, and the most wild maybe not just her dialogue but image as well changes though that assumes we enter the pregnant sex tag.
Just some ideas... also who are you working on now I assume you finished Shaymin lmao.
(Addendum, Caitlin owns the villa Cynthia is in so instead of bumping into her Caitlin provides you access after figuring out you're the father, thus meaning THREE potential Cynthia ship dialogs, one where she is oblivious to the fact you were even there because you didn't breed Caitlin, one where she is disappointed you didn't come by to see her despite breeding Caitlin and the one you get for doing the side scene. This idea just keeps getting better.)