It's not that I dislike "linking to a file from the HTML editor", it's that I dislike using the HTML editor at all. Or, I guess more accurately, I dislike being forced to use the HTML editor in order to access what used to be basic Moodle features.
You're right that it's straightforward to make a link - still significantly less straightforward than linking to course files was in 1.9, but perfectly reasonable - but in order to do it, you have to know the capability is there! There's no reason for any reasonable user to suspect that the "link" button allows you to upload files to a super-secret file area associated with the assignment.
More importantly, as I've discovered, there's no management interface for the super-secret file area. This results in bugs like http://tracker.moodle.org/browse/MDL-26388, frustration on the part of assignment writers, and confusion for students when they have to download a file called "assignment_version2.pdf" instead of "assignment.pdf" because Moodle decided it didn't like the name "assignment.pdf" anymore - even though, given the way Moodle's file systems work now, the file by definition can not be used in any other scope and there's absolutely no reason why it shouldn't just be replaceable with a new upload.
Assignment
Making a file available to students
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