Just for my two cents, I always thought it was strange that the raw ingredients and completed food items weren't separated. I suppose the reasoning would be that more advanced recipes typically involve combining one or two raw ingredients with an already completed food item, and there is that oddball Swordfish Steak.
The other thing I thought would be kind of cool is allowing you to combine two recipes if you have three cooking slots available. Let me explain using letters in place of ingredients to avoid spoilers. Let's say you want to make food item D, and the "recipe path" is to first cook ingredients A and B, then take the result and cook it with C to get D. In other words:
(A + B) + C = D
What I'm suggesting is that the game should, if you have three slots available, allow you to do this:
A + B + C = D
...thereby allowing you to produce D with one cook instead of two.
The only problem there is that there could be some instances where that would be ambiguous. In this case, A + B + C means (A + B) + C, but it could also mean A + (B + C) or (A + C) + B. It may be all the same in math, but I don't know if there are any recipes in Aquaria that conflict in this way.