The more I've thought about it since, the more I think we should represent images with hexagonal pixels (i.e., laid out on a hex grid), and that color images should treat the center points of red, green, and blue subpixels as not being right on top of each other. (the third image in the post shows how they would be arranged, which is actually similar to how they are on some displays)
It would be a little harder to deal with for graphics programmers who are working at a pixel level, or at the least, it would require a bit of relearning. But it makes more sense in so many ways. Hex is just a better way of "circle packing" (as you notice if you arrange a bunch of pennies on a table), and of course real world displays tend to have the red, green and blue subpixels offset from one another anyway. (are there any that don't?)
Obviously it isn't easy to change something like this at this point, but still, I find the idea fascinating, and appealing to the OCD efficiency fan in me.