Apps hasn't lived up to its initial promise. Yes, webchick is fully entitled to say "I told you so",, as is Open Outreach developer rosemarymann, another early Apps sceptic.
Anyway. In practice, few apps are realistically usable outside of the distributions they were written for. In the Debut set, we have current usage of ~135 for the http://drupal.org/project/debut_apps module--the only way that Debut features can be installed as apps outside Open Outreach.
Panopoly is only minimally using Apps. Most Panopoly features have been removed from Apps, and those that are offered as apps have many dependencies that are not provided via Apps and so effectively can't be used via Apps outside of a distro.
Now that we're introducing Panopoly apps, the Apps install UI will be even more cumbersome, as it will require at least two - possibly three - screens, one for Panopoly Apps, one for Debut ones, and possibly one for Open Outreach ones. All that without access to what we had in Subprofiles: install streams, grouping of features into streams for common use cases (membership site, event site, mapping site, etc.).
Remove apps install time usage. Replace with Subprofiles. Consider enhancing Subprofiles if/as needed.