I believe Jetpack's approach is already a bit similar to the CBOX plugin: once you have installed the plugin, you can use all the modules, or only some of them. If you don't need one of the modules, you can deactivate it, and it won't be called or used on your site. Its settings won't appear anywhere in your dashboard.
If you want to use Jetpack without having to connect your site to your WordPress.com account, we have added a development mode to Jetpack to enable modules that don't require a connection. This feature is not available in Jetpack 2.2, but you can already test it by downloading the development version of the plugin. Once the development mode is active, only the modules that don’t require a WP.com connection can be activated. See r676269 for more details.
You can develop add-ons and plugins on top of Jetpack (see my profile for some examples, or search the plugin repository). Some people have actually forked some of the Jetpack modules into stand-alone plugins.
You can also contribute code and submit patches through Trac:
I hope that answers some of your questions. We're open to feedback, and I'm always happy to read what people have to say about our plugin!