10.1 NukeNPave or Upgrade

I selected upgrade and the installer wants to remove almost 100 packages from my basically "stock" 10.0 Retail installation. The remove list include the latest version of Adobe Acrobat 7.0. Doesn't look like a very clean upgrade. If one chooses to do a fresh install "Nuke N Pave" any recommendations of what to backup beyond one's home directory. Personally, I would like to a clean upgrade without having to rebuild the world. Nuke N Pave belongs to that other operating system.