It seems to me there are several specific problems with the reply-to-comment boxes:
1. The boxes do not allow the user to change their userpic, spell-check, or preview the comment without taking additional steps which, previously, were not necessary.
2. There is, as of now, no way to disable this feature and go back to the old system.
3. The "more options" button takes you to an unstable URL which can't be bookmarked for later reply. Replying to a comment of mine in this community leads to:
Which will expire. On the other hand, the old system (or using Open in New Window) takes you to a stable URL which will work permanently:
4. When you click on the "Reply to this" link, the box opens even though the status bar in your browser indicates you will be sent to a URL. If you use "Open in New Window" it follows the URL. This is very inconsistent behavior, and is not good UI, in my view.
Some people like the reply-to-comment boxes, and I don't think the idea is necessarily a bad one. But it should be an option set by the user (by which I mean the user replying to the comment, not the owner of the journal).
In general, it seems this feature was rolled out without a lot of thought. It should be rolled back in until its more prominent shortcomings are fixed.