So, I think this boils down to two enhancement requests for the publish command.
1. There should a "Batch" option (much like the Batch render command) to simultaneously publish several different sets. This milky means another pane in the Publish dialog to select 'saved sets' the than just sheets and saved views.
2. When creating a new Sheet Layer or a new Saved View there should be an opportunity to add those sheets/views to saved publication sets. Currently the sets have to all be redefined to add content. This would be similar to creating new design layers or classes and adding to (or excluding from) exiting SLVPs. This new functionality should also be accessible via the Organization dialog?
Do these need to be two different enhancement requests?