For my thesis I had some similar ideas, but they were more abstract, sculpture-like. The user volume was a cylinder, with varying radii (mapped to activity) at different heights (time). The mappings you are talking about are very subjective, but it's good brainstorming. Refining and iterating over such ideas, brings innovation.

You are spot on that Github has very rich relationships of collaboration and sharing that are not all expressed by the data I chose. I wrote a longer post about my goals and motivation with Ekisto that addresses that concern: http://processq.tumblr.com/post/69098066993/ekisto-design

I also write about future work which will improve the current version. I think some tagging functionality either precomputed or user-contributed will help a lot of newcomers understand the map better. Stackoverflow veterans immediately recognize the clusters and the avatars.