One thing I'm really annoyed about: after ever Reader update (Win7) the once deleted shortcut icons on desktop and in the start menu reappear. And they can only be removed with administrative permission.
Please: an updater should not generate new shortcut icons. It may update existings shortcuts whenever a path changes, but otherwise please honour a customers decision.
While I started to replace Acrobat Reader with a less intrusive PDF viewer wherever possible, I still search a way to avoid this clutter.