Sub-folders under applications are absolutely essential. The Intranet module, for another example... Building large, complex packages by composing existing packages is an excelent way to re-use code. It perhaps makes more sense than some of the service packages we have now, like General Comments.
Here's another hurt for ya:
* Sub-site admins can mount any enabled package on the system.
The old ACS' closest equivalent was the group pages, where when creating group types and groups you could specify which applications a group admin could later mount. (speaking of group pages, we don't have any... I think we need a group/group-type package...)
As it stands it's probably a security risk to allow untrusted users admin rights over a sub-site, which is a shame. No ASP style ACS...