I love the SEO concept behind this plugin and have been using it for over 5 years with modifications. I recently built a new version at http://wordpress.org/plugins/blog-comments-seo/ because this version wasn't updated for ~3 years.
The recent update has not fixed the issues below, looks like the only change was removing the link back to the plugin authors site that was added to all SEO super comments pages (not allowed to add a link back that way in a WordPress plugin in the repository).
My new version fixes the canonical URL issues and removes the need for the template file also fixed a bunch of out of date WordPress code (depreciated code and various PHP notices). Also changed the way the links to the super comments are generated which should mean my new version works with all themes. If you read through the support requests here you can see users discussing the issues which I've fixed.
The original plugin stopped working correctly when WordPress core added canonical URL support, this added a canonical URL to all the SEO Super Comments pages back to the main post: this means Google will find and spider the super comments, but won't index them, will pass the SEO benefit etc... back to the main post.
If you aren't familiar with canonical URLs to Google they are like 301 redirects minus the browser redirect: stays on the page, but SEO benefit is passed to the canonical URL.
You could fix this issue in the original plugin by creating a single-2.php template file and a header-2.php file and have single-2.php use header-2.php as it's header. Within header-2.php you could add the PHP code to disable canonical URLs: the super comments pages wouldn't have any canonical URL. This is not needed in the new version at http://wordpress.org/plugins/blog-comments-seo/ you can still use a template file, but it's not needed, your themes single.php template file will work out the box.
If the new plugin becomes popular I'll add more features, there's a lot you can do with the comments SEO wise.
Big thanks to Vladimir Prelovac for creating a great plugin in the first place.