Hello again. Some remarks and answers.
i feel like it would work better to have the computer aim for an atp production a little higher than its consumption, probably scaling with the size of the cell. basically higher by enough that the cell won’t be left in the dark if it tries to heal an injury or duplicate a part, but not too high to where it is burning way more food than is necessary for it to survive.
This is very unnatural as an aim, but this is however something I’d like to see emerge. Remember that we want to replicate natural pressure, and that we will thus try to make them be by bottom-up interactions from basic mechanics. So yes, but too complicated as such.
you gain the ability to engulf at a relatively small size (which, by the way, is insufficient in itself for sustaining a newly added nucleus might i add), the difference in hit points between big and small cells is virtually nothing, and most of the parts reserved for big cells are either mere upgrades of more basic parts, or simply unusable by the AI.
I agree with you on the nucleus part, some rework is needed and it is under discussion. But as I’m starting with the start, I’m currently working on early mechanics and thus prokaryotic evolution. Nucleus isn’t even a thing to me right now ! 
there really isn’t a whole lot of incentive for having a very big cell.
Although not to that extent, natural selection does incentize small size overall as well. But I’m working on giving bigger cells a little push, as I said.
some qualities of “prey” that the computer may want to look out for
1.) small enough to be swallowed whole by big cells
2.) lack of offensive parts like spitters or spikes around the front parts of the cell
3.) peaceful and flighty behavior
These are very complicated things. It will be of relevance latter, but that’s a level of complexity too far away from what we have today (except engulf size which is already implemented).
you obviously don’t have to listen to any of this if you know it’s not gonna work out. just trying to help out a little is all.
I still try to do it, first because it is nice to engage with the community, but also because writing this helps me clarify things out. Last, some input can also be useful, and may also show misconceptions about the game from the community, which is always good to keep in mind.
Last but not least I appreciate your efforts, thank you.
Should you want to dwelve further into the matter, feel free to have a look to our dedicated files for auto-evo! Link here : Thrive/src/auto-evo/simulation at master · Revolutionary-Games/Thrive · GitHub