The warning "What are some of the issues with ccsm and why should I not use it?" is referenced in a lot of answers. But no alternative to it is proposed anywhere.
What are the alternatives ?
In 12.10, thinks seems to span between gconf and dconf (and maybe elsewhere ?). I was not able to find the real place to set focus follow mouse for example (metacity gconf option seems to do nothing).
Most of the settings in CCSM can be altered/changed using gsettings command. dconf-editor is a graphical alternative to it also. But both of them requires some knowledge about the backend system.
MyUnity and Ubuntu tweak was great (limited), but I heard they get removed from 12.10.
Here is the manual page for gsettings
For example, to change the font from Ubuntu 11 size to Ubuntu 10 size, you would execute this command:
gsettings set org.gnome.desktop.interface font-name 'Ubuntu 10'
You can install dconf-editor with the command sudo apt-get install dconf-tools
Update: Ubuntu tweak is back now!! That is a great news actually. So happy tweaking !
There are actually a handful of alternatives to CCSM. Here's a quick rundown:
Current:
New since 2013, still being actively developed. For some reason it's the only one in the official repositories. To install (for 13.04+):
sudo apt-get install unity-tweak-tool
Past:
