This is the big one to me. It's much more difficult to search for specific content if it's isolated amongst communities on different servers, all trying to fill the same niche and splitting the potential userbase for said niche up between them.

If there was like a tag system in place that communities could use to tag themselves as being for a specific thing, like cooking, for example, and then you could aggregate/search posts from all communities under the cooking tag across all servers federated with yours, it would greatly simplify finding content for less tech literate users while also increasing the resilience of the entire network by allowing more communities for a specific niche to exist, which would prevent content loss if one server goes down without discoverability being an issue.