Crouton is actually a breeze to use. While the crouton script itself might have a few hacks under-the-hood, the end result is quite slick. Everything just installs under `/usr/local/chroots'. Removing one of your potentially many chrooted installs is just an `rm -rf'.
I prefer keeping ChromeOS primary and just opening a crosh window to expose one of these chroots (a browser and terminal is similar to my work environment on a Mac). Granted, XFCE can act weird if you choose to launch it, but I've never needed that functionality.
If you do want to completely replace ChromeOS, there's Chrubuntu.