Its a fundamental difference.
Consider HTTPS, SSLv2, SSLv3, and TLS1.0, and TLS1.1. As web security standards evolved, the people who run HTTPS servers flat out refuse to upgrade the security protocols. Federated admins don't necessarily run their servers as a full time job, while centralized organizations are well funded and well paid.
It takes a lot longer for infrastructure in federated networks to upgrade. Facebook can add new features across the entire network immediately.
Imagine if you wanted to add a game protocol to IRC for example. You'd create the protocol, then you'd try to get Freenode to switch over to the new and improved game protocol, and then they won't do it. So you create your own IRC server and no one comes. You give up and open source the project. Years later, some guy finds your open source implementation and maybe the protocol finally becomes popular enough to be used... or maybe they'll use your protocol as a base for their ideas and it will evolve into something else.
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When "federated" works, it is mostly due to the big players agreeing that a particular federated protocol is amazing. Take OAuth for instance, which got Google, Yahoo, and Microsoft support early.
Ultimately, it is very difficult to make money from federated services, so there's no money (or investment) going into those projects. OAuth was a pro-bono non-political effort to make the web better. Such efforts are extremely rare.
In fact, most federated protocols exist to give a particular company an advantage (or to levy disadvantages on a particular company's competitors). So there's a healthy amount of distrust to any newly proposed protocols... for good reason. Ex: Theora / MPEG4 / video tag nonsense, or DRM support in web browsers.
The big daddy federated network: Email / SMTP, was basically a research project from the late 1960s, and received public investment in the 1990s as IMAP and POP3 protocols were developed. (Anyone else remember paying for Juno email on their 33.6kbps modems?). Due to years of use, it has found its niche and no "competitor" will ever really displace it.