App.net is controlled by the users. Facebook and Twitter are both controlled by the advertisers. App.net is not. It is an open platform, meaning that developers could build apps based on its API. Now, you’ll say: but I can do that on Twitter and Facebook! Oh no you can’t.
Twitter and Facebook’s APIs are not open. For a number of Twitter APIs (such as Site Streams) you need to be explicitly granted access, and that’s very very difficult to come by. Facebook is generally the same. On App.net, I believe the APIs will be open for developers to use in their own apps for App.net. I’ve been told by a backer (I haven’t backed it yet, since I’m a student so therefore, skint) that people have already started doing this.
App.net has the potential to change the social network industry, On the service, you own the content, not the App.net management. On Facebook, you are simply a product that uses the service. Two completely different ends of the spectrum, and I know which I’d prefer to be part of.
Yes, for the first part of App.net’s existence, there may be only developers on there and people like me, but I find that a good thing in many ways. It means I don’t have to see the rubbish I see on Facebook, like baby photos and people going OMG I GOT SO DRUNK LAST NIGHT. Meanwhile, on Twitter, I get UberFacts and OhWonka. At times, those are good, funny things to read, but I don’t want to see them all the time. Sometimes, I want to talk with like minded people, which is almost impossible on Facebook and increasingly difficult to do on Twitter, since 90% of the users on Twitter are people I don’t want to talk to. The other 10% are the type that would back App.net.
Hope that clears things up. tl;dr the service (you call it a Twitter clone) will diversify as time goes by. But what really matters here is the under-the-hood stuff.