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 One thing I love about being Catholic is that the church's structure is very decentralized. We never have to care about the Vatican or the bizarre, evil, and bewildering things that go on there. Is the Vatican a disgrace? Yup. Is it just another example of the corruption of concentrated wealth and power? Yup. Does it change my faith or beliefs? No, it has nothing to do with them any more than Washington DC represents me as an American. My church exists through and for my community. I trust the people and priests there. If not for the internet we'd never even hear about the Vatican. It's a shame that the ostensible head of the church is so corrupt but I won't leave Jesus on account of Judas. Just my 2¢ 
 Maybe churches just aren’t that centralized in general, but I think the Catholic church actually is one of the most centralized. Only beat by maybe the Mormons. 
 I think you mistake the protocol for the implementation. Catholicism is extremely consistent at a protocol level. I can go to almost any Catholic church in the entire world and experience the same Mass, even at the Vatican. That is the protocol. The implementation is the church, the people and priests there, how they operate, how they act, what decisions they make for their community, how they build trust, etc. Every church is funded by its community; no church gets money from the Vatican to operate. In this way each individual church lives or dies by its community. In this way it is as decentralized as it gets.

The Vatican rarely messes with the Mass and when it tries to there is global pushback. Resurgence in the Latin Mass has come from a grassroots interest, for example, not from the top down. 
 Hmm yea. Resurgence of Latin Mass is a great example. Definitely shows that there is an operative bottom up principle. I have heard however that the Pope can unilaterally remove any priest. That seems more centralized than other churches.