The best thing to do to "counter" this coming centralization is super easy to do, but from my short time observing here, it won't happen:
1. There should be stricter criteria for an instance being listed on "join Mastodon." Insufficient moderation gets you de-listed. Handle cynical false reports.
2. It should be easier for a new admin to just check a box and opt-in to a whitelisted federation that excludes the worst instances.