Thanks for the feedback! I implemented several of your points including saving a design and reloading it at each layer, shrinking the membrane, updating some of the tutorial details and menu text to try to steer the player better around compiling and recompiling, the economic overview on ATP and NAD+ production/consumption (you can click on either element in the top bar and it will pop out the rates), and a link in the tutorial to the field guide entry for that step to provide more detail, while keeping the tutorial text a little more constrained.
I'm still thinking about your point #4 - I did make a change from another comment about diffusion below to try to make that function more consistently when resources are being shared between two consumers. If you play again, let me know if this new version feels better or if you still feel like the whole diffusion system needs a redesign.
I also got some feedback that the look and feel were lacking, so I updated that as well. I went for a stained slide look with microscope magnification transition animations between layers. Hopefully you like the new look, but if you have any feedback on that, or anything else, I'd be happy to hear it!