I appreciate your efforts, but I'm not new to game development. XD I like your way of looking at it. I see it the same way. =3
I have worked on several small projects before (for maybe 15 years?) and I've talked with many devs. I've also been participating in the CataclysmDDA project recently.
I'm an artist, though. I draw and write. Coding and level design have been my main focus, and I've worked on some pen&paper RPGs and board games. I have never finished one, but as you say, it's about the journey. XD
With this I wanted to make something fairly simple to code (that's why I use javascript, so I don't have to worry about handling rendering and event pools) and with a focus on the story and a single solid mechanic. Obviously, the mechanic will need some expansion from what I first considered, but that's ok. =)
About the money, I don't mind how the resource is called, but what I don't want is for it to be a "everything can be derived from" kind of resource. And since I looked at it in a more board game perspective, I realized some games that do it the way I want, like Arkham Horror. So I think I know how to attack that front now. =3
Due to the background of the story, minions are a bad idea. Besides the point that I don't want exponential progression to happen too aggressively, if at all, you're supposed to be alone in this enterprise, not being able to trust anyone but you. Reading your document I realized that's a pivotal point in the story. It is you alone, fighting an abstract entity that is not even a single person or organization. You could call it fighting society, but it's also not quite right. You're mostly fighting the statu quo, like heroes and villains do, but as the story unfolds you'll see that's not really what you're doing, though the ending depends on your actions, of course.
Also, you are supposed to have an almost limitless supply of basic materials, so the reason to breed cats is not because the cats are important or useful directly. It's because it's the only way to see what a given genetic makeup produces as a phenotype. In layman terms, making the creature is the only way of telling what it can do from a cryptic, uninformative piece of data. The important part is the genome, but that's (easily) inferred information, not given straight to the player.
And it is not "alien cats", though some shapes they take might suggest that. It's mere greed that spawned the ultimate genetic manipulation technology the player will encounter. =P
So I would say you could sell cats(genome), but only in order to obtain other breeds that you didn't have access to. Maybe later you could obtain a tool that makes some task easier, but not if it's as a limitation to the way the game starts. Though tying into the above idea of expanding the lab, maybe you could buy too some automated weaponry to prevent infestations. That sounds like a deep puzzle mechanic that could be easy to implement.
Having a limit of 5 cats is a tentative and could be as easily 10 or 7 or whatever number. Of course, you can store as many as you want, but you can have only a limited number active. Or risk having them loose. The point of that is both to tie in the mechanic of creatures being potentially dangerous with the aspect that you're not actually caring for the creatures. They're a means to an end. And there's also a path (several) in the story where you're forced to ignore that limitation, thus balancing risk of losing the game in two different ways.
And furthermore, thinking about that made me realize I could include a feature similar to a New Game+, but instead of having it when you win, you have it when you lose, so you can recover faster from a loss while not breaking the story or mechanic progression. Whatever genomes you store away in a game you lose could be available on the New Game+ at some kind of black market. That way you can get back to the part of the story you failed at as soon as you have the ability to potentially do it, but without going though all the process again.
I don't mind savescumming, but I guess it would be nice if it just is not necessary. Also, the idea of the player having the improbable possibility of chancing upon a endgame creature by typing randomly in the genetic code machines is too amusing to pass up. =P