Well, the main advantage of distributed comment systems has always been the idea that people who stumble upon your site are already logged in and therefore more likely to leave a comment. Anything - absolutely ANYTHING - you can do to lower the barrier to participation is good.

As such, the value of any one system largely depends on how many users it has: how many users will arrive at your site, see their own gravatar smiling back at them, telling them that they are already logged in and that any comment they contribute will earn them rep within the larger system. Any rep system used by a large number of sites is going to encourage people to comment more frequently.

Now that the merge between the IntenseDebate and WordPress.com userbases is underway, IntenseDebate effectively has 12 million users - at a stroke, it has become the most useful commenting system. If the rep system is also deployed across all WordPress.com blogs, Automattic will have a home run, no-one will be able to match that momentum, IntenseDebate will become the standard.

My only reservation about IntenseDebate it lacks the killer feature that makes Ajax Edit Comments (the comment plugin Jeff uses here at the tavern) really shine: the countdown that allows users to fix mistakes in their comments that they didn't notice before clicking Submit.