Calypso does not yet have a plugin architecture for extensions, but even when it does, it will be completely incompatible with all existing WordPress plugins that integrate with the WP admin. This works for WordPress.com because it doesn’t support arbitrary plugins and so they have a fixed feature set that they have to account for. This is not the case for WordPress.org, so unfortunately there is no easy path toward adopting Calypso as the next-generation admin interface for WordPress.org.
I personally think the Customizer provides a good foundation for bringing us forward. But I don’t know what the community thinks, and obviously implementing this would require buy-in from the entire community. Should we use the Customizer as the foundation, or should we start from scratch like Calypso? I favor the Customizer (obviously) because it is something we have today as a foundation and we have existing themes and plugins already supporting it, and so we can better continue our commitment to backwards compatibility.