I plan to make this film in 3D CGI. My previous 3D film has a relatively clean look, but with my thesis I'm trying to create a very textured, worn look and "dirty" up the frame. The 3D elements will be created in Maya, and I'll likely composite in Shake (maybe After Effects). Although the characters and environments will be 3D models, I'm going to experiment with rendering them flat - sort of like a textured Toon shaded look. Hopefully this approach will also have the side effect of keeping my render times lower than if I went with a Global Illumination-type look, which in turn will give me more time to play with the art directing.
In addition, I'm going to use a lot of handmade (possibly animated) textures along the lines of the references and tests that I posted about earlier. I'm also looking at puppet/stop-motion films for character design ideas. As I've mentioned elsewhere, I'm going to do some tests with Massive for the crowd scenes.
Finally, there will probably be a tiny bit of live action in there too. During my Contemporary Topics project, I got some more experience integrating a live cloak onto my animated character. Similarly, I used some dry ice footage as fog for my last film. Based on these projects, I feel that elements like dust (which I plan to have a lot of) are a lot easier to create in live-action than in CG, and can be integrated pretty well with some careful compositing and futzing with the frame rate. Live elements also seem to ground the animation, and make the environment seem more believable and organic, even when you're not going for a photorealistic look.