The biggest issue with using a custom theme is that it gets out of date. The bootstrap theme modifies the majority of the templates, so it's especially succeptible to this. I'm thinking about how to allow people to use themes without that drawback. Here's the plan so far. Each theme can include a special file that specifies a URL to get a theme-specific template schema. WSN's manage templates page and upgrade.php can then check that URL, which will return an array of standard uniqueness hashes for theme-customed templates. For templates the user hasn't altered, upgrade.php will automatically replace them with the latest version of that template for that theme. When a user clicks 'revert to standard' in the template editor, the template will revert to the standard for the theme rather than the standard of the default theme. For templates that the theme hasn't altered, the template editor and upgrade utility will use the default theme standard versions so that there are no problems if the last theme update was a few versions back.

I think this plan should significantly improve the experience for people using themes other than the default.