In an update to my original post on commenting systems and SEO a recent Hangout On Air with Jason T. Wiser covered the question from the point of view of the end user.
Pulled into it along with yours truly were Google Authorship expert and Stone Temple Consulting director, Mark Traphagen and Developer Donart Nummer.
The main take aways here were the main criteria for choosing a comment system for your blog:
• Ease of implementation
• Engagement increase
• Tracking (the comments)
• Social value (depending on your audience)
Watch the video for the main discussion: