This post is split into two parts: what we want for 0.3.1, to be released as soon as this and bug testing are finished; and what we want from cytoplasm in the final game.
So a cytoplasm organelle has been planned for a while now, and according to @crovea it's relatively simple to do but nobody's gotten around to it yet. Effectively it's a blank organelle, which will require its own definitions and an extra organelle panel in the left-hand scroll section.
My question to the programmers is this: are you planning the simple route of adding a cheap blank organelle that just adds size to the cell and consumes small amounts of ATP, or are you going to have it be a base organelle which needs to be placed before adding others? My thinking is that the latter might be too complicated a concept for players to handle until we get a tutorial or better GUI in place, but the former doesn't serve much purpose.
Either way, I guess it adds things in place for future modifications, and since it's the last part of 0.3.1 left I'm hoping it can be completed within a couple of days.
For the future, we need something that actually serves a function. To an extent, even a blank organelle that does nothing but change the shape could be a creative tool, but it seems redundant simulation-wise. If membrane generation stays similar to what it is now, you don't even need cytoplasm to build a shape - you let the membrane algorithm fill spaces in for you.
Here's every major mention of cytoplasm in the GDD in relation to itself and other mechanics. Of course these things can all be changed, but I think they serve as important reasons why cytoplasm is so important.