Paper has been optimized for Unity and includes styles for the Unity launcher and dash. However the experience when using Unity is slightly different and some apps may not have the same coloured headers as on other desktops.
Paper works great with on the latest version elementary OS and the Pantheon desktop, with the bundled Plank theme you even get Papery goodness on your dock..
GNOME is where Paper is best and bundled with Paper is a theme for GNOME Shell that is designed to compliment and be an extension the desktop theme.
If you're using the fledgling Budgie desktop, Paper also works great on that.