I like what I am hearing from Nate about what a Next Generation Journal should look like. Nate is right that “because we can” is not a good reason to make changes. We have good reason to streamline the peer-review process. We also have good reason to streamline the publication by eliminating the bundling in favor of publishing articles as they are cleared for publication and there is something to be said for publishing post-publication comments. I see no reason to publish pre-publication comments because if the comments are still relevant after publication they may be added to the post-publication comment list.
The only other change that I think would be important would be in changing the model for the distribution of rights to the intellectual property. This would most likely be based on the work of Creative Commons with the author(s) retaining rights to the material while granting specific publication rights to the journal which would have to be defined, but which would probably not be hard to nail down.