I would prefer to be able to install and upgrade all apps through the Application Manager. I am not familiar with AppStore, but here are some improvements I would want to application manager:

1) The ability to refresh application list for a single repository, or a list of selected repositories. (Not too important for me, but if that was obvious to the average user, it could help them isolate a repository with update issues.)

2) The ability to browse applications available for install by repository. This would be especially helpful when installing third party repositories to quickly find what you just added.

3) More detailed descriptions of packages, or hyperlinks within the description to a page with more details, screenshots, etc. Much like the Maemo Downloads pages now.

All I know from my experience is that whenever someone says "Oh, a new version of XYZ is out!", I check my application manager for an update or package first. If I have repository.maemo.org for chinook (or whatever), I should't have to go to a webpage on maemo.org and search through to find a link that just opens app manager back up.