I think we would all love a fully integrated stats solution like Wordpress.com. But as you said 2 years ago such a plugin would not be easy to build.
So what's about the following suggestion:
You have a cool Google Analytics for WordPress Multisite plugin. Would it be possible to add to this plugin the ability to view the Google Analytics stats directly inside the WordPress dashboard of our network users? That would be really great and easier for our users and might be a closer step to a fully integrated solution.
The Google-analytics-dashboard plugin (which doesn't seem to be an adequate multisite solution) might be a good source of inspiration.