One problem is that when uninstalling programs through the stock application manager it doesn't remove it completly. This could easy be adressed and should be considered as a bug. (i think?)

Instead of sending a "apt-get remove" call it should be optional to send a "dpkg -P" call. So the program and configuration files get purged. This can of cource be done manually too but would not be adviced for a newbee.

On a normal linux machines this is not necessary as the memory inprint would not be so much. It does however exist some program for it. And considered the small hdd on the n900 might be a good thing.