I think the splitting of mastodon into federated communities is a bad idea.
I think this because the communities are isolated and this naturally generates division and clashes among different groups of people.
While I don't currently see huge problems, I can see this getting worse as more people join the social network.

I'll take the Italian community as an example, since that's what I know best.
Italian mastodon is split into several different communities, the largest are generalist.
If I'm not mistaken, the largest three are: mastodon.uno mastodon.social mastodon.bida.im
The first one proclaims to be the official mastodon instance for Italy and many people from the other instances disagree with this.
I'll analyse this particular conflict, which appears to currently be the largest one in the Italian community.

I'll refer to mastodon.uno as the main instance and others/outsiders for all the other Italian instances.
Not all Italian instances are involved in this debate, but most of them are; there is maybe livellosegreto.it that stands a bit more neutral.

Other instances look down on the administrator of mastodon.uno and often criticise some of his actions.
The admin of the main instance condems the other instances for being anarchists/rebellious, it is true that some of these instances host some anarchists but that definitely is not the scope of those instances.
The admin of the main instance sometimes responds by blocking/silencing people at an instance level.
Going forward, this hate towards the admin migrates towards the users of the main instance.
Thus you will get people from the other instances discussing with each other about how bad the users of the main instance are and often insulting them.
More often than not these are just generic insults directed towards nobody in particular.
However, since most of the people engaging in these behaviours are being blocked by the main instance, most of the people that are being insulted are ignare about it.

You thus get a system in which according to the instance you choose you'll be induced into hating certain people or you'll receive insults solely for your instance choice.
It becomes normal to make jokes about mastodon.uno users, for no particular reason and new people joining get used to it.
Now, this is just a petty fight about the ideology behind instance administration and the discussion is mainly about some bold claims and practices done by the administrator of mastodon.uno.
However, this system could get much worse when instances with different ideologies get to clash with each other.
At that point you'll get real radicalisation of people.

I don't think there's a solution to this.
Defederating an instance might work only when it is getting started; defederating gab has no real effect since it already has enough people to self sustain.
Deciding to defederate a small instance is however hard and won't probably work, since people will be skeptical about closing their doors to someone who is just starting out.

All in all, I think the system is flawed and that no solution is available to avoid these problems from arising once many users join.
I offer no solution.