I think having a few types of herbs, colorcoded based on their medicinal effects. So for instance red for healing, blue for mind increase, green for spirit, etc etc. Any potion would then be categorized into what kind of medicinal effect it is in accordance with the herbs, and that type of herb would be needed.
Beyond that, what I would find interesting is to have bigger, more potent herb species in each category in each biome that are more difficult to aquire and cultivate. The more potent potions could then be made using the more potent ingedrients of these flowers, or by destilling the medicine from lots of less potent herbs (this also gives you a way to use the many herbs you hoard, although it is time consuming for your herbalist as to incentivize cultivating more difficult herbs.) Size and colour would be an easy way to convey to players the complexity of this system, so I don’t think it is that heavy. It might be useful to go for a kind of complexity that matches farms.
Example for game elements in aquisition: say “lifeblossom” is a healing herb of the “very potent” variety. It is a blossoming tree whose berries have high medicinal healing powers. It only lives in certain places in the highland biomes, and other “very potent herbs” would live only in other biomes. Which means that highland towns can be very lucky with finding one in their direct surroundings, or might find a gerenal trader reasonably quickly to get the seeds from another place in the same biome. Non-highlands towns would need to aquire it using the special “seeds from a distant lands” mechanic, which will be very desirable. Meanwhile “mildly potent” herbs can be gotten from general traders, and can also be found in the world by chance, and every biome has every type of herbs of this potency. Lastly every map in every biome has the little “lightly potent” herbs of every type.
Example for game elements in cultivation: Building off of the gathering zone idea of @Pawel_Malecki, we could instate a dark green “garden” zone. This zone can be specialized to three types; a herbal garden for the herbalist (for the cultivation of herbs), a wood production zone for workers (so the saplings from the nursery farm are automatically grown and harvested in a designated spot) or an orchard (if modders or ACE wants to add fruit for some reason). A mix is of course also possible. What the specialsation is is determined by what plants the player places in the zone.
This will take micromanagement out of the cultivation of herbs, as most plants will be maintained by the relevant hearthlings using “harvest and replant”, both whenever they need it, as much as they need it, and without players issuing harvest commands (which is still possible of course). However, when it comes to herbs, the game element will be trying to create biodiversity in the garden, and designing its contents and layout. This kind of biodiversity can be necessary to cultivate some of the more potent herbs, or you might demand that the the very potent herbs from other biomes be grown next to plants from the same biome, so that the soil will look like the soil it is used to. Most playes tend to make these types of gardens already to have herbs near, so I don’t think it is a stretch to attach game elements to this.
I also agree with @YetiChow that incense and aromas are interesting to use for more suble or specialized effects (again, based on types of herbs). Much of the above will be just a little too complex if potions have their current use, but if using the wonders of the natural world is rewarded, and getting/growing the herbs isn’t too much of a grindy or hoardy pain, it can be a good addition.
And there are many ways to reward this type of gameplay. The gardens or insenced bathhouses can be places where hearthlings seek social time, distraction from emotional pain, or to relieve the stress of being unneccesarily put on town alert all the damn time. I belive we now have weapons that can inflict wounds (debuffs) on enemies, so our hearthlings might get these debuffs as well and need longer recovery that usual (for which specific herbs might help), and aromas can imbue places in the town with subtle effects that help out their hearthlings. Maybe a hearthling will unconciously carry more things if he feels fit. Adding depth to hearthling wellbeing can have plenty of opportunity to make all of this worth it.