It's been a while since I've set up a BSD system, but Upstart on Ubuntu isn't that complicated in its hierarchy.
Startup scripts that actually do work are still traditionally in /etc/init.d/
The configuration files, telling when services are to start/stop/etc. are in /etc/init/, rather than /etc/rcX.d/.
doesn't seem too much more complicated to me. I believe the benefits of Upstart are great; its use cases at present are well justified. I haven't contemplated whether I agree with it taking over mounting drives or cron, though. Also, it needs to document its uses, setup, and syntax FORMALLY (example wikis are not enough, Scott!).