I‘d like to point to an argument I‘ve made in another thread two years ago in light of this discussion:
The consensus back then was to have the smallest 3D organism be 1cm instead of 1mm, which I very much understand in retrospect. But that decision has ramifications for this discussion, namely: How is the smallest possible 3D organisms (ie the macroscopic starting blobs) motility hindered by the amount of oxygen it can get with diffusion alone?
The answer I have in mind is illustrated by flatworms. They can be up to 9cm long, but their body is extremely thin, 1-2mm at most, because they don‘t have a circulatory system and rely on diffusion for gas exchange.
This presumably represents the maximum thickness viable for motile organisms which rely on diffusion. For this reason I suggest that the player starts the macroscopic stage with an organism that is 1cm long, but qiet flat (~1mm).
This works quiet well with how the macroscopic stage currently starts, as it simply scales up each cell to represent a metaball. I suggest keeping the transition like this and making this flat starting organism able to move without muscles, relying solely on organelles line flagella and cilia for locomotion (which aren‘t be visible at this stage). But this flat mobile organism would need to develop a respiratory system and muscles in order to develop a thicker body (which could provide space for more complex organ systems) and still be able to move that thicker and heavier body.
I‘m not sure what comes first in this cascade of developments. Do muscles evolve which then necessitate dedicated respiration? Or does respiration evolve which then im turn allows gas-exchange-heavy muscles to evolve? Either way it feels like these are somehow tied together and are necessities for mobile organisms whose thickness crosses the threshold beyond which diffusion alone is no longer viable.