Even assuming Twitter doesn’t go all evil on us, there are going to have to be some changes even to maintain the current level of useability (whatever your opinion of that). Even if the userbase doesn’t change, the rising popularity of linked apps will result in a steady traffic increase.
As with all those Farmville (etc) updates on Facebook, endless automated tweets from Instagram, Foursquare and old favourites such as Flickr and last.fm could easily become the noise that overwhelms the proper content on Twitter. Of course, you can unfollow or block anyone instantly, but these automated tweets could just as easily be coming from your best mates. It’s all about being selective.
On Facebook, it’s a trivial matter to filter updates from specific apps, so a person’s regular status updates are unaffected, but no such option currently exists on Twitter. Rather than worrying about third-party developers using their API, Twitter’s next move should be to incorporate some of the filtering and muting features already provided by Nambu, Echofon and others.