The save and reboot function didn't/doesn't? work for me either. Well up to the shutdown part it did... Didn't test them since though and can't remember if it worked before.
More of a feature request: What do you think about making the app more of a theme manager. I mean adding features like downloading themes and icon sets and maybe fonts via apt-get/wget, preview them before download. Possibility to change everything indipendently without having to mess about with the files... It would be the best (in my opinion) if themes and such wouldn't even show up in the default app manager, although thats probably not up to you or me.