The downside of using a forum system for comments, is that:
- the user probably has to register with the site to post a comment
- the user may not have single sign on ability through Vanilla
- you won’t be storing your comments in a system that can export them and import them into another commenting engine, like Intense Debate or Disqus.
- you’re giving up the ability to use Facebook Comments–that’s if that’s important to you.
- you lose all the moderation settings under Discussion, and you won’t be able to see your comments in the WordPress admin against posts in the post editor, unless somehow you figure out how to program that in. It’s important, so you can approve/deny or spam comments. Plus, you may not get the benefits of Akismet.