I agree, the current reply form looks really clunky and breaks the vertical reading line. Why not use something like WYSIHTML? (http://wysihtml.com/)

When I created my first reply comment and submitted, it showed up twice on the page through the AJAX call. It was fine after refreshing the page, so it didn't get submitted twice. It seems to be a bug in the return function. I opened the page from a submitted time link.

A couple of years ago there was also a lower adoption of html5 elements. Having one h1 tag per page is still a good Idea in general, but it is allowable to have one h1 tag per containing article tag as well. Since this theme does not seem to use tags like article and aside (that I've seen in my quick check) I agree that there should only be one h1 tag per page which contains the page title or headline. The theme structure is otherwise good, but could definitely use with some contextual revamping of quite a few divs.