Summary of relevant responses:
- The funky directory structure is here to stay
- There is no way to turn off autoloading
- This is done for backwards compatibility
Backwards compatibility is good, and actually if I were to start an extremely simple app right now I might still want to use autoloading.
I still think it’d be nice if there was something you could put in a config file to turn it off. Or I guess meteor doesn’t have config so a meteor package you can add to turn it off. Sounds like a difficult package to write… if someone writes it, I’ll use it 
Woohoo for 1.5! I’m hoping I can use the new features to load different css for different routes, but that’ll be another thread…