There are only two features I miss in the application manager:

1) (not critically important) - an option (enable/disable) to ignore any currently off-line or failing repositories and just go ahead and update the package list anyway (like apt-get does). No more checking the logfile and disabling of repositories (which you then have to remember to re-enable at some point).

2) (important) - a third selection to show the _new_ packages since the last update (in addition to the existing two for upgrading and looking through everything). Now I update, then I check for upgrades, and then I have to wade through the whole list and try to spot something new. The command-line desktop application 'wajig' has such an option ('wajig new' in addition to 'wajig new-upgrades') - extremely useful, and more so when the list of applications grow.