uWSGI requires another daemon which you must manage. With uWSGI, you must configure Nginx to forward requests to that daemon. Phusion Passenger fully integrates into Nginx so that is no longer necessary. With less moving parts, there is less system administration overhead.
The uWSGI project solved that "issue" (really, i have difficults calling it an issue, but i can understand the point of passenger guys) with the "uWSGI Emperor" more than one year ago in a pretty elegant (and system-friendly) way. You may want to look at it.
Yup! I already use it - I have templated config files so I just create a symbolic link when creating a new Django app.
I didn't have to configure Emperor mode on my new Ubuntu machine - it has a directory where configs are stored. I remember 8 or 10 months ago, you had to configure emperor mode and set the "vassals" directory, not anymore I guess.