I actually found it to be the opposite for me, I found it easier to set up shots and camera movement because from watching anime and editing clips from it I kind of got the sense of how the camera should move and what kind of compositions look good. In fact I think setting up the camera became my favorite part of the film process when I started taking production classes. Now lighting I would say we are spoiled on, I really wish I was better at lighting, I guess its okay since my film style tends to be a bit darker and gritter though.
I really like the begging of it though it was almost like a movie, and I do agree amv editing does give you an advantage on editing in the intro classes (our school called it Production 1). This is my most recent short film though done for a project in my junior project class if your interested in checking it out.http://www.youtube.com/watch?v=yEKjdZvuank
Well, it's important to note however that a lot of shots you see in anime, while common in film, are uncommon in anime. Most of my exterior shots as they pile out of the truck and set stuff up are moving glidecam shots. These are uncommon in anime cause in anime they are typically budget blowing CG/crazy entire background animated moving shots. The same kinda shots that get cherry picked to use in AMVs, even if they're pretty typical following shots in film and television.
...And, maybe it was just me, but while I understand the combination of background and foreground somehow made 'A pretty picture', I had to put a lot more effort into learning composition AND depth of field. Particularly as depth of field is a matter of not just composition but understanding camera operation as well.
Lighting though, that's a fun one. It can be fun to do scenes but also time consuming and lighting is expensive stuff. Right now I only use my school's gear but I intend to blow some $700+ on a three piece LED lighting kit to use once I'm fully independent.