The current idea is that only ancestral wild forms of plants will exist in the beginning, and people will have to hybridize them to create optimal crops.
The original idea was to have plants in neighboring squares crosspollinate at random, then you would gather the seeds and see what grows out of them. However, making evolution totally random doesn’t sound very fun. You couldn’t guarantee that your plants would develop in the direction you want them to take. You would basically have to grow plants without knowing which mutations the seeds carry, then rip off the ones you don’t want to pollinate anything.
What sounds like a better idea to me is having a system where a player can choose an aspect to boost knowingly. If other plants in the location already possess this aspect to some extent, you have a higher chance of succeeding than if you are trying to mutate it.
You would click on a feature and if you are lucky, it gets a boost in the next generation. However, things have their consequences, so for example if you boost fruit size enough without boosting stalk strength, the stalk will eventually bend or snap under the weight, causing the fruit to touch the ground and be exposed to rotting. Likewise, there might be a cap to fruit sugar content before you have first improved the root and leaves. To me, this seems much more game-like and entertaining than merely deciding which plant is next to which.
Also, if you manage to create a seedless hybrid, you either need to figure out a way to breed it asexually or keep the parent strains alive and continue crossbreeding them, hoping to get another seedless child.