Removing features to decrease maintenance overhead is also a pretty legit reason, and you don't have to be a corporate site for that to apply to you (I would say it applies even more to a hobby site).
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.
Also, “it’s not used frequently” is a really bad reason to remove a feature. Frequency of use is not a proxy for usefulness. I don’t use my backup software’s “restore” feature often but that doesn’t mean it should be removed.
Standard MO of software engineers is to rewrite code into the latest and greatest framework/language/style every couple of years to keep the resume fresh.
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.