These issues are best addressed on the Sublime Text forum, but for the first one at least, .py files in a subdirectory under a package won't be loaded as plugins, so you can place libraries there (this is done for Packages/Default/send2trash, for example).
The plugin's unload_handler() isn't run when quitting the app, which isn't very nice. @atexit.register also didn't work.
The plugin also won't reload when the source is changed. At least when there is a symlink in the Packages directory pointing to the plugin folder.
But the editor seems nice and will be a good editor after some UX and API work.