My complaint is actually not with ST3, but with Package Control. I have to maintain my user preferences in git because PC rewrites them and resets the theme every time it updates. (I run the Material Design theme)
This might possibly be fixed by using PackageResourceViewer. It allows you to edit the package files for themes and have your changes stick. (I use this to change the font size for the tree on the left in the theme file, and I only had to make this change once).