@meandmy10, think of the CPA system as the statistics (who your prey is, who eats you, what your death rate it), but you're right. Thr player probably only need to see it in the editor when he is thinking about what mutations to make.
As for deciding which compounds to show I think #3 is the most flexible choice. We can order the compounds based on their priority to the cell (we already have a number for this) and display the top 4 most important compounds the cell uses. Then, when the player presses the plus icon, we give him the option to drag and drop additionaly compounds to the bottom of the UI. I see two ways how we could do this:
1) When the player drops a compound from the + menu, the compound that is to the very right (glucose in your image), gets put into the + menu, making sure that we always have eactly 4 compounds showing
2) When the player drops a compound, he now has 5 compounds, with the fifth one showing up on the bottom of the UI. He can then choose one of the 5 and drag it over to the + menu, or leave it like that if he prefers to view 4 compounds at the same time.
Another idea that I just came up with: Instead of having the + button open up the small menu thing, we could have it "extend" the row of compounds and make multiple rows showing all of the available compounds (for those hard-core players that want to see everything). The plus button then becomes a minus button, and when you press it you once again see only the top 4 compounds. Just like in the previous versions, you can rearange compounds by clicking and dragging them where you want to place them.
Anyway, I'm starting to really like this UI. Cannot wait to see how it turns out!