I'm trying to tread as carefully as possible with this concept, because it does introduce an intriguing concept that could work, if carefully executed. With modern taboos toward incest kept in mind as we proceed, the idea of royal intermarriage for Bannerlord is an interesting idea. European royalty is already related to each other whether it's through second or third cousins: Charlemagne is considered Pater Europae and Queen Victoria the grandmother of Europe. I'm not fully aware of brother-sister marriages or its prevalence in the early European medieval period, but there's no doubt about first-cousin marriage or other notable inbreeding examples or effects: the Habsburg Jaw/Habsburg Lip, Charles II "El Hechizado" of Spain, the practices of the Bourbon, Wittlesbach and Braganza royal families. However, the inclusion in this game would be controversial since people would immediately proclaim that TaleWorlds approves of incest, regardless of the historical context of royal intermarriage and inbreeding. But second and third cousin marriage can be a viable option and even first-cousin could possibly be implemented, if done carefully. There could be a system regarding intermarriage and eventual inbreeding, with its own penalties (diseases like haemophilia, infertility, shorter lifespan, life-threatening diseases, appearance) and benefits (consolidating political influence within the clan, fiefs, keeping the bloodline "pure,").
It's definitely just a small brainstorm, but if implemented carefully, it could be an interesting mechanic.