I find Nautilus' GUI much more to my liking than Unity, and I've been having a lot of problems with Unity, like the menu bar at the top disappearing leaving me with no file specific menus on maximized apps, and no controls for audio volume, no clock, no shutdown menu etc. (have to use power button to pop up Shutdown menu). Plus Unity seems to run much more slowly than Nautilus - or is that just 12.04 in general?
Nautilus is a file manager while Unity is a desktop environment that uses Nautilus as its default file manger and to display the desktop background. As they are quite different things there is no way to replace Unity with Nautilus.
If you don't like Unity you may have a look at other desktop environments like Unity 2D (installed by default), Gnome Classic (install package