Right now, gpk-application (now known as "Packages") is bundled as a part of gnome-packagekit. Since we now have the new Software application - which is installed by default - it would be confusing to include gpk-application by default as well. Two GUIs for installing software would be really weird, and could really confuse users ("which one am I supposed to use?!")

My recommendation would be to split out gpk-application into a separate package. This way people can install it and continue to use it if they really want, but it won't get in the way for those who aren't interested.