There have been other removals, but few of them were of even specified features, and I don’t think any of them have been universally available. One of the closest might be showModalDialog <https://web.archive.org/web/20140401014356/http://dev.opera....>, but I gather mobile browsers never supported it anyway, and it was a really problematic feature from an implementation perspective too. You could argue Mutation Events from ~2011 qualifies¹; it was supplanted by Mutation Observers within two years, yet hung around for over a decade before being removed. As for things like Flash or FTP, those were never part of the web platform. Nor were they ever anything like universal anyway.
And so here they are now planning to remove a well-entrenched (if not especially commonly used) feature against the clearly-expressed will of the actual developers, in a one year time frame.
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¹ I choose to disqualify Mutation Events because no one ever finished their implementation: WebKit heritage never did DOMAttrModified, Gecko/Trident heritage never did DOMNodeInsertedIntoDocument or DOMNodeRemovedFromDocument. Flimsy excuse, probably. If you want to count it, perhaps you’ll agree to consider XSLT the first time a major, standard, baseline-available feature will be removed?