Here's my stream-of-thought on the matter......
I love documentaries, and an AMV Documentary is something that always comes to mind whenever I catch one. It would help you if you've seen a lot of different kinds of Documentaries, to get an idea of how you would like to structure this one. Are you going for a "Fan" film, like the recent ones on Bronies (i.e.
A Brony Tale,
Bronies: The Extremely Unexpected Adult Fans of My Little Pony) or more of an educational/historical perspective on the evolution and influence AMVs have on otaku culture, like the documentary series
Metal Evolution?
You're essentially making a video about editing/re-mixing (copyrighted) video and music, so I would be miffed if you didn't include something about the legality of the hobby which has had some run-ins with the law in the past (remember Evanescence). You could possibly reference
Lawrence Lessig and watch his TED talks on remix culture and cultural creativity, one of which he actually plays an AMV as an example.
I'd would like to recommend you also check out other documentaries about "Film", for inspiration and to get an idea of how they incorporate movie clips into telling their stories. After all, I assume an AMV Documentary would actually show some clips of edited AMVs...right?
The Cutting Edge: The Magic of Movie Editing
Side by Side: The Science, Art and Impact of Digital Cinema
These Amazing Shadows
Beyond that, I strongly recommend watching
DEMOGRAPHICS: Behind the Scene, a short documenatry that explores the definition and roots of an artistic computer sub-culture known as the demoscene, very similar to the AMV community and their creation of Anime Music Videos.
Both Brad and Radical_Yue offer interesting outlines on a possible direction for a story, with a focus on fans and creators, as you'd expect. But I always felt the history of AMV creation also incompassed more than just the people. It's about the
ANIME (why are some titles used so much in amvs?). It's about the
MUSIC (why the hell does everyone use Linkin Park?). It's about the
VIDEO (we've gone from VHS tapes to DVD/Blu-rays to Digital just within a few decades!).
So how's this for a quick brainstorm....what if you broke the documantary into those constituant parts and actually talked about each aspect of it with fans and editors (why this Anime, why that Music, why this Video source?) and how it all comes together into this massive community we call Anime Music Videos.