So many of the file location problems are solved by something like GoboLinux. I would like to see more effort in this very straightforward directory heirarchy.
I would like for my OS to handle my files for me, much as package management systems handle my executable programs for me. I would like to a "pictures" section that includes all the pictures on my computer, regardless of where they are located.
Ubuntu freed me from having dozens of installer files on my desktop. However, I still get dozens of images, documents, and videos strewn all over it. Ubuntu: help me manage my life and I will love you more.