I have Noticed one change in my home folder. Now there are some new folders like ".adobe", ".cache", ".cinnamon",etc., and files like ".profile",".bash_logout",".xsession-errors", ".gscan2pdf" etc.
These are hidden folders which are only visible in your file manager when you enable "View Hidden Files"
It may not be what you want to hear, but if I were faced with the situation you described, I would not hesitate to install Mint 16 and forget about Mint 13.
My own experience was that I installed Mint 16 on a trial basis, and found that I liked it so much that I could not go back to Mint 13. That was even though I had Mint 13 configured just the way I wanted it - like you did.