1) The root menu / start menu is horribly outdated. It's basically a less functional version of the Start Menu Microsoft shipped with Windows 95. It needs an integrated run/search box at minimum.
2) It would probably make sense to combine Applications/Places/System into one menu. It wouldn't preclude you from doing it separately if you wanted to -- there needs to be a panel app that offers an all-in-one setup and it should be the default.
3) Nautilus has way too much wasted space. The breadcrumb bar and toolbar should be smaller by default. In fact, the toolbar for all GTK apps should be smaller.
4) Part of the wasted space problem is fonts. The default GNOME fonts are just too big. They need to go down -1pt at least.
5) On post-install the user should be presented with at least a few different color/theme choices. The orange/brown thing really doesn't work. It's fine to include it but at least have an option of something different the first time a user logins in. Many people will never take the time to carefully customize themes. There should be several pre-built & tested color variations.
Other than these 5 suggestions I think they've reached a nice level of stability and consistency with the Ubuntu/GNOME UI. It doesn't need any major changes -- just some refinements.