I want to make two points.
1- I am against this general idea of the microbe stage having a linear progression. You start out weaponless and then develop weapons in the above order while upgrading your organelles. I think this will mean there is basically 1 playthrough of the stage and once people have done that then they are done and waiting for the next stage. I think we want to be looking at simulator games for inspiration. IMO you should play once (as say a big photosynthesizer) and look at the small fast cells and think, "that looks really fun." So you start again and play as a small fast cell and see other cells using agents and think that looks cool so you start again and play as an agent producer. I think the best thing to be should be whatever everyone else isn't doing. If everyone else is giant cells with all these crazy features the best thing to be should be a small cell with 1 flagella, you can just go round hoovering up resources while outpacing these big cells. IMO the game needs to be paper-scissors-stone and not a race along a tech-tree, because basically you can only do that once. For this reason I think every upgrade needs a drawback.
Now this is just a suggestion, I don't care if we make this or not, it's just an idea. What do you think? Does it sound fun? Remember the goal of the project is to make the most scientifically accurate thing we can which is fun. Fun comes first.
2- What I have been suggesting for this is to have 3 "archetypes" and push the advantages and costs of different improvements in such a way that you are forced to choose between them (of course you can be anything you like but IMO a cell that has everything should be super weak). So the 3 archetypes would be
a. A large cell with lots of melee damage pilli on it. It can command an area of resources and is much stronger than
b. a small fast cell (imagine a sperm) with a single pilus. It can run from the large cells but can't defeat them. It can, however, run down and catch
c. agent producers who are medium speed but are able to produce a lot of different agents. They are unable to escape from a small, fast cell but can take time to destroy a large, immobile cell.
so a. beats b. beats c. beats a. The gameplay then becomes about range control (who is faster) and how much hp and damage you have (hp can either be raw hitpoints or, much better IMO, a model of how well your cell is functioning with osmosis pumps etc). If you choose to put everything on your cell then you become big and slow and you burn so much protein making agents it's really hard to grow / reproduce so you become rubbish. I think this is a good system because it goes on forever. You need to adapt to whatever niche is available. If everyone else is big and slow get agents. If everyone else has agents then become small and fast etc.
Now this is just an idea. I am totally happy for this not to be made or for us to be make anything else. However I do think it is a mistake to go with a linear, upgrade based, pathway. It might be more realistic (in terms of microbes developing) but we need to think about re playability and fun (because this has to last for years before the next stage is finished).