Had a couple of ideas that are sort of related to Gen 6.
First something I have a feeling you already thought of. I think it'd be funny if, whenever Groudon and Kyogre go Primal, Rayquaza shows that she's been able to go Mega this whole time. Little reference to how Rayquaza doesn't need a stone for it.
Second, something based on someone else's Zygarde suggestion long ago. Something like a Ship Scene orgy where Zygarde splits into 5 to 10 10% Zygardes who are each less pregnant than the normal 50%. Original suggestion suggested something about sex with the individual cells but I can't find it so I'm not sure if I hallucinated that comment or not.