"Packaging" is a talent agency bundling up different creative roles (writer, producer, actor) for a project (film or tv show) and then pitching that group of people for that specific project to the studios. The agency takes a percentage of the _project_ revenues instead of a percentage of each individual _talents_ pay for the project.
This is apparently the standard way things work in Hollywood now and has some consequences:
1. It screws up the "Agent" part of the talent agency. They no longer directly represent an individual's interest (like a Real Estate agent or a Lawyer) because they just want to get people into a "package". This is the main problem described in the article, that there are some massive conflicts inherent to this process.
2. Packaging projects make agencies way more money than directly representing clients.
3. It reverts movie and tv making back to something like the studio days. Every actor isn't really able to work with every director, in order to get something made they need to be "packaged" which means working with someone else from within the same agency.
4. It messes up people lower on the rung more than top tier folks because they're less able to buck the system.