I don't think a federated wiki is solving any of the problems of wikipedia. You've just made a wiki that is more easily spammed and will have very few contributors. Yes, Wikipedia is centralized, but it's a good thing. No one has to chase down the just perfect wikipedia site to find general information, just the one. The negative of wikipedia is more its sometimes questionable moderation and how its english-centric. This has more to do with fundamentally unequal internet infrastructure in most countries than anything though. Imperialism holds back tech.
I agree that it might be fine for niche wikis but again, why in the world would you ever want your niche wiki federated? Sounds like a tech solution looking for the wrong problem.