Actually there are some annoyances about aggriculture.
1. Seed-Storage
They take a lot of space and you have to scan them to know what seed you get. So I suggest a machine, that doesn't work like an inventory but stores scanned seeds as data, not as item.
Basically the machine as two slots. The input slot is where you place seeds you want to store. If you place a seed inside this slot it get's stored inside the machine, if it is not fully scanned it is instantly moved to the output slot.
The machine has also buttons to search. One for the type of plant and three for the GGR-Data. You could set this to specific plants and GGR-Values or set placeholders to search more general. If you're done with specifying your search you could start the search and it will show you what seeds are stored that fulfill your search-request and how many of them are there. For only one output-slot you could then select on of them to be placed into the output slot (with more output-slots you could retrieve more seeds at once.
2. Seed-Scanning
First the cropnalyzer should detect weed as weed, would make things easier even if weed is easy to differ from the other plants. Second a stationary analyzer, or improvements to the cropnalyzer are really welcomed. I guess there is a reason that the cropnalyzer does not have an internal EU-Storage like most tools and that the GUI is not able to interact with your inventory. This makes analyzing crops very annoying. A stationary block would at least ease it by not needing energy. Since mobile energy-storages and seeds both don't stack inside your inventory getting rid of at least one of them would be really nice. I guess you have already some ideas about this.
3. Some obvious plants
I suggested barley to make beer as a plant, since I felt some obligation to suggest it due to being german. But still there were plants in my mind that I actually did not suggest since they were somehow obvious. One of them is bamboo for some sticks and the other is cotton. Both are real existing plants, which would be a plausible source for wool and sticks. They also don't feel as strong as something like an Uranium-Plant, which I some dislike (and since there is no UUM-recipe for uranium I guess there will also be no plant), but it seems reasonable to have some source for sticks (although you could chop down some trees easily), exspecially if you find a way to make the sprite sheet not that limited.
4. Balancing farming vs. breeding
I really like it that you have to spend some time on breeding. Breeding should be hard. Getting better plants and creating superior kinds of their species should be a lot of work. But I'm actually not sure about the actual farming. Personally I somehow dislike some of the stronger plants, but I guess you made up for this by making it hard to reach the ressource-dropping final stage of growth. But totally destroying plants if you forget to hydrate them is something a bit annoying since it is so hard to tell if something is well hydrated/fertilized. I would prefer if plants grow "backwards" if the conditions are bad. Maybe it is also possible to give conditions two priorities. So if plants like to have a certain lightlevel, hydration etc. you could define some as "does not grow if not fulfilled" and "does slowly die if not fulfilled". So you could simulate real plant behavior a bit more efficient (...well maybe this already happens).
If I assume that you have some plans for aggriculture too, I'm most likely right. Maybe you thought about some of the things already, but maybe you could drop a bit of information why you have chosen certain designs, since some of them feel a bit strange, but might be due to coding restrictions or maybe to surprise us with a better MkII-Version.