FTP was never integrated: it just so happened that some platforms shipped a protocol handler for it, and some browsers included an FTP protocol handler themselves. But I don’t believe you could ever, say, fetch("ftp://…").
Flash, like applets, was even more clearly not part of the web platform. It was a popular third-party extension that you had to go out of your way to install… or wait for it to be installed by some shady installer Adobe paid off. Though I have a vague feeling Chrome shipped with Flash at some point? I don’t remember all the history any more, this is a long time ago.
Older versions of TLS is definitely a more interesting case. It’s a different kind of feature, but… yeah, I might consider it.
<keygen> was an interesting concept that in practice went nowhere.