I feel like the system should at least start in the m/s range, and not immediately jump into km/s. Most humans find single-digit km/h speeds pretty challenging.
Take out the Christian symbolism and I'll rate it higher. You'll have other favorable reviews if you don't I'm sure, but it does make the game less fun for me.
After the main quest line, consider adding in procedurally generated paintings with randomized names to keep things going.
Also, you can't go wrong with adding in ways to spend prestige points. I think you've got solid potential here, please keep adding onto it!
After a certain point, breeding speed becomes largely irrelevant and is overshadowed by the low mutation chance (after gold/green and green/blue, imo). The stash size becomes the limiting factor on new mutations, when you develop 6 plants every second or so.
The swooshy motion of all the ingredients is hell on my processor. Maybe a little fade animation within the box so you're not making twenty screen elements would be better?
Did anyone else notice that the sign when you first pick up boneless wings outside, you know, a wing flanked by two boneless ones, looked a little suggestive?
Of course, if you really want, you can also just hold spacebar in the swim and run training courses to spam them... but why would you when you can feed the cute little duckie?
it's the mistake that I've got to know long after game developing and getting rid of it would be really time-consuming :/