And that's exactly what's supposed to happen. Instance wars and eventual defederation and fragmentation are important moderation tools, and will progress the culture and feel of instances and regions of the Fediverse. Many instances will form federated cliques that are highly connected and have similar vibes and cultures, and some will be federated with multiple cliques, showing users a variety of cultures and situations.
If the Fediverse reaches a large enough number of people, it can support multiple independant cliques, and enable users see entire mini-universes with different communities and vibes.