A"custom network type" would be a phenomenal addition. WordPress Multisite in itself opens many possibilities to create web applications more than a standard WP install. Managing users, sub-sites/blogs and access at various levels is amplified when WP is used in multisite mode.

It'd be awesome to build on top of the current features and provide in-built support to creating Custom Network Types or at the very least create multiple networks managed through a single WP install without having to resort to using rudimentary plugin based solutions.