Jon, I have a request that you may or may not be interested in implementing.
Currently there are a number of plugins that load up custom gutter icons. ST3 currently still uses the old way of loading gutter icons; they must be relative to "Theme - Default". In the past, when a plugin was creating a region, you could just feed in the custom icon like so:
Where custom is an icon named custom.png
With the sublime-package format, this is impossible since the icons are now inside an archive, but regions require the icons to be a path minus the png extension.
Ideally it would be nice to give an icon path not relative to "Theme - Default" if the icons was provided with a path like "Packages/MyPlugin/Icons/custom" (keeping with the current convention used everywhere else). And it would be doubly nice if the API simply did a load_resource() on the path to retrieve the icon so it would work for sublime-package archives as well.
Currently, plugins will have to unpack icon resources themselves and also must create a dummy "Theme - Default" folder to allow the region command to find the icon relative to the "Theme - Default" and not fail.