Changing to a 3D Microbe Stage has been suggested many times, but as @tjwhale said, all our existing mechanics and the engine are built around a 2D movement style, at least initially. Compound cloud diffusion in three dimensions would be considerably more difficult to program in 3D, for instance. So while this is an impressive-looking concept, unfortunately it's unlikely to influence the game design much.
I do like those bacteria(?) though. Were you planning to do more work with them?