It also took me so long to fully grasp what was going on lol, but I am actually quite fond of the concept here, and the mechanics are SUPER creative and unique!!
Perhaps a more visual wrapper around things & some sort of tutorialization would have gotten me past the confusion. Like a preview of what each card will do if you apply it, on hover, for example.
In terms of balance, once small change I'm thinking about is, maybe the total mass of the root system would be a better metric to use to track the progress towards flowering?
I would love to see the flower sprout at the end, atop my final root system! Perhaps different decisions the player makes would lead to different types of flowers, or something.
But gosh this simulation environment is so neat, I want to build a whole garden from it!