That said, I really hope favorites isn't removed because even though I only discovered the feature a few years ago, I really cherish the comments I've favorited.
...Exactly. It's been a feature forever, it complicates the codebase, and no one ever uses it.
Two examples[0,1].
Hardly ever see it used in any capacity though.
Re gp: removing buttons shown on every page is probably more about simplifying interface and reclaiming space than maintenance overhead.
The humane reason, of course, for removing features, is so you can add new ones while staying simple. I have always found this to be a deep part of, let's call it, healthy software development, at every level. If you remove things as well as add them—code, features, complexity–then the system can breathe over time. When I say "the system" I include the programmers and the community as well as the code—the whole thing. If you're only allowed to add, that's no longer a creative process, just agglutination.
And fortunately, I didn't suggest that we do, or that features should never be removed... rather that removing a feature that people use because not enough of them use it doesn't make sense for a site like this.
If you want more people to use new features, I think you need to put more effort than you do into making those features more visible. Feature discovery is a problem - there's plenty of anecdotal evidence here to attest to that.
I can think of a couple of possible solutions, such as having new features be bold for a while after being first introduced, so they're more easily noticed, or pinning a thread announcing new site features, or having something like a devlog listing possible and new changes and comments related to development, to better engage the community in the process (or at least raise their awareness that the site is still being actively worked on,) etc. Or all of those.
That's something you do with a corporate site where you're constantly A/B testing and aggressively removing features that don't generate revenue. Hacker News isn't (or shouldn't be) run that way. It's perfectly fine to have features only a few people use.