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).
Best Answer
There are actually a handful of alternatives to CCSM. Here's a quick rundown:
Current:
Unity Tweak Tool
New since 2013, still being actively developed. For some reason it's the only one in the official repositories. To install (for 13.04+):
Past: