Before you upgrade get your system exactly how you want it (meaning the packages you have installed). Once you are happy open a terminal and type
sudo dpkg --get-selections installed-packages.txt
Make sure the file is in your /home
Now do your upgrade and then type this in a terminal
sudo dpkg --clear-selections
This will clear the newly setup list in apt of what packages are currently installed on your system.
Now type this into your terminal
sudo dpkg --set-selections installed-packages.txt
Now all you should need to do it
sudo apt-get update
sudo apt-get upgrade
This will uninstall packages you don't want and install new versions of the packages you do want. All your previous user settings should, if you have a separate /home partition, be in your /home as .hidden files (the . indicates the file/folder is hidden)
The relevant information is in the man pages and also in various places on the net.