Script
As already mentioned, The Matrix borrows a lot from centuries-old notions of philosophy - and throughout the film, you can see constant references to it if you look closely enough - while managing to aptly meld this with a firmly pulpy sensibility, resulting in a weird and rather brilliant action film. It's got colourful characters, amusing dialogue, and a strong arc, leaving us wanting more just as any great film does. Inception has an insanely original concept, and the problem with that, as one can expect, is that it requires explaining a lot to the audience to ensure they keep up. Thus we get one of the areas that Inception received complaints about, that Christopher Nolan makes little effort to hide the expository moments, and essentially uses Ellen Page's character of Ariadne to have everything explained to the viewer. It's not the most subtle way to weave a narrative thread, but at least Nolan has the good sense to make fun of it, notably when Ariadne asks mid-mission, "So, whose subconscious are we in now?". Despite Inception's less-subtle story beats, it's the overwhelming originality and water-tightness of the story, as well as its character-based elements, that allow it to pull ahead of The Matrix, which is nevertheless extremely successful as a pulpy actioner that just doesn't get the heart engaged in the matter.
WINNER: Inception