I think some people are also confusing the terms "manually manage" and "automatically syncing with selected playlists, artists, and genres".
There is no good reason why I can't have Genius Mixes show up on my iPhone if I am syncing automatically with selected playlists, artists and genres. My iPhone can't hold all the songs that iTunes includes on the 12 (or even 4) Genius Mixes even when only transferring those playlists.
The Genius Mix feature should really just be a database of songs that fall under that category. When you click on the Genius Mix on your phone, it should just play whatever songs from the database are on your phone. Argh!
I agree with you.
This seems like it would be easy enough for Apple to fix. Send them feedback, everyone, and hopefully they'll fix it soon. (9.0.1?)