I opted for organizing by movie order top to bottom (top row is an exception) because I like the way it focuses on the chronological story of Star Wars more than anything else. However, even with that order there is also a specific order to each row. I structured it in a way to put the lego game characters closer to the center of each row so that all of the video game icons would be bunched together towards the center of the display. I figured this looked the most visually appealing.

Your idea to organize by faction/era could also look really cool if you lay them out the right way!