What I found is that choices have been taken away in the latest version. And, for me, that means I can't ever upgrade again.
I don't use Windows' Programs folder to installl applications. On my XP system, Atlantis and all the other apps are installed in C:\MyPrograms. Atlantis' documents are stored in C:\MyDocs\AtlantisDocs. I only use the My Documents folder for junk files. My Win 7 computer has a similar setup.
From what I've read, it seems that if I upgrade, I will not be able to install to the folder of my choice, and that the documents will be saved to a folder designated by the new iteration of Atlantis, not where I want them. Is that correct?
Oh! My feature request: Give us back the choice of where and how to install.