Nestling cells inside of one another would be really cool, so players could build up little organelles. Also, some clarification on the different products you can make would be nice, I'd love to see if they would have any interactions/reactions if certain ones were in the same space. Maybe cutting down on the number of products that can be produced so each feels like it's got it's own niche -- I would love it if one of them gave you resistance to toxins so that you could ingest that product and break it down like food.
Also, I had a quick question -- When you break things down, do they turn into arbitrary energy units? Or could they become separate products (and energy units)? It would be cool if "Food" was just a collection of the basic components, but by breaking it down you made the byproducts, which could be toxic in higher concentrations, encouraging the player to spit them out or distribute them at certain levels. I'm not sure if it would be possible, but making the cells expel junk in one direction so that it'd be easier to fight gravity/move would also be nice, or maybe making some products more efficient at performing certain actions would be cool. I shared this with a few of my friends from college, so I can see if they'd have any ideas, too. :)
That's probably a lot of feature creep and the balance might get messy, I've just been thinking about making a game similar to this for a while and it was so cool to see something like it. My brain kinda ran wild once I played it, there's a ton of potential.