Wow, I thought that up close the kindle display would look like a honeycomb, with each cell having a black blob that pops up or down to provide contrast. Seeing the chunkiness of it makes me wonder if they are making the crystals smaller to allow for better color separation to improve contrast, or just improving the colors of the crystals, as previously mentioned.
According to E-Ink, the company, each microcapsule is roughly the width of a human hair. In this explanation
http://www.e-ink.com/technology/howitworks.html, they mention that "These microcapsules are suspended in a liquid 'carrier medium' allowing them to be printed using existing screen printing processes onto virtually any surface, including glass, plastic, fabric and even paper." This probably accounts for the less than perfect arrangement. Incidentally, I e-mailed them last week and asked how many microcapsules there are in a 6" display. They haven't yet responded.