Centralization is a problem because it gives a single entity total control. That's why Twitter was able to screw with third-party clients in the first place, and why it mattered that they did it. Take e-mail as a counterexample: Google, for example, couldn't really screw with third-party e-mail clients, and even if they did, people who want to use third-party clients can just switch to a provider that isn't stupid.

App.net retains all of this control. They merely promise not to abuse it. I'd much rather not have to trust anyone's promises. Even if they remain completely honest, their idea of abuse may not match my own.