I remember a while ago you were thinking of a negative side to botania, as flux/warp is in thaumcraft. My idea is Weeds that grow adjacent to flowers and cause unwanted side effects if not properly maintained, and controled. Weeds could slow down the mana generation of flowers, or cause effect flowers to do things like return tiled dirt to plain dirt, Looniums could be forced to spawn zombie flesh or other junk items. Weed would have a great chance to spawn the more flowers of a certain type are present, and/or when high amounts of mana are used. You could even have them affect players, by blinding them or poisoning them.