I haven't played Botania enough to consider all the content, but ways I would tweak what I know of Botania to be more like what I think of GregTech:
Change the petal recipes: Initially, petals can only be crafted in a player's crafting grid, at a rate of two flowers for one petal. Automation only becomes possible once the player has crafted a pair of manasteel shears, also improving efficiency to one flower for one petal. Enchanting the shears with silk touch increases the output by an additional petal per flower. Higher-tier materials may provide better output as well.
Change the Petal Apothecary: Crafting now takes time, and the rate of progress depends on the level of sunlight received. At full sunlight, it takes about a minute to finish, at 8 sunlight (accounting for both time of day and obstructions), it doesn't operate at all. This can be reduced if the player spends mana or creates infrastructure, only reaching instantaneous speeds at endgame tier setups and mana input. At some point, there is an option to easily automate the setups. Perhaps plant flowers nearby, send mana into a certain block, and the block will non-destructively take a petal from each flower (with significant cooldown, such as a full day to allow them to "regrow"), and try to craft the result of combining all of them.
Change crafting in general: Most of the more advanced items can only be crafted if certain plants are present in a 7x5x7 area around the crafting device. The presence of certain other plants blocks the recipe. Which plants affect each recipe varies, requiring players to either set up multiple partially-specialized crafting stations of each type, or manually switch out the environment on occasion.