I think you're asking some questions I've already answered.
Alright, I'll back down on having the species name there. I don't get why everyone is so drastically against it seeing as it's already in the game and so won't take much effort to copy for the new GUI, but if that's the decision fair enough.
I did say there'd be a confirmation box. It could slide out from somewhere given certain conditions, but for the sake of player agency and choice I think it should always be an option. If they know they're going to lose ATP gradually with no hope of recovering it, why force them to wait through the entire process? If their species is on the brink of extinction waiting will only diminish the number of individuals available to switch to. Granted, if that happens switching to another individual may not be much better, but in my opinion the player should always have the choice.
I put the editor button there so it would be next to the reproduction meter. It's a purely aesthetic choice, but it means the player can see each bar fill up towards the goal of being able to reproduce.
Maybe, that hasn't been decided upon. I said the way to get rid of the box would be click somewhere else (think the right-click menu on most computers), but there could be a dedicated close button.
It slides the reproduction meter in and out from the top of the screen. Some players may prefer not to have it on-screen at all times, but it needs to be quick to access. Not sure about the editor button sliding in, it feels like there should be a permanent button for such an important action (that gets greyed out when the prerequisite compounds haven't been collected).
Perhaps that could work. The problem then is that the player has to open the compounds panel, scroll down to each of the compounds they've chosen and un-toggle them there, which is actually more complex a process than clicking on those already visible.
If we set a maximum number of compounds to display, yeah, otherwise with a lot of bars they'll end up being too small to understand.
It opens a new window over the top of the game (with the game paused) showing all the compounds and the process links between them. I'll mock up a basic design based on tjwhale's idea, which I think is really quite neat. It'll allow the player to turn processes/organelles on and off as well as spending locked-up compounds to repair them.
I don't think that's the best idea, again because the editor button is the most important button and the player should be aware of it even when unavailable.
EDIT: Here's that mock-up of the processes panel:
tjwhale's original concept was a sprawl of compounds and arrows showing every process in one diagram. That might be possible but it'd be pretty damn difficult to fit everything on one diagram, and it creates a problem for modders who want to create their own organelles and processes. I've tried to fit the same information on something modular to solve these problems.
On the left side are the reactants for each process. Those which can be stored are represented by their storage bars, whereas others (like sunlight, and actually water now that I think about it) are just the names with arrows. In this more detailed view, the compound bars could have lines on them showing the levels above which compounds would start to be vented.
In the centre are the organelles responsible for the process. I think each process only occurs in a single type of organelle, so correct me if I'm wrong. For every organelle your cell has, another arrow is added (so in this example, the cell has four mitochondria, two chloroplasts and one of whatever the organelle is that performs pyruvate synthesis). Organelles can be turned off by clicking the black box on the arrow, becoming grey (like the first mitochondrion). If an organelle is damaged, it will be highlighted red, and clicking it gives the option to spend locked-up compounds to repair it. This removes the need for any sort of organelle healing UI in the environment itself.