Here's some ideas:
* Completely omit any mystic flowers from blooming. Instead, use Agricraft hybridization to make you have to cross-breed your own flowers. Also, require a specific soil which mystic flowers needs to grow on that is only player-created with a suitably obnoxious recipe. You can also cap the growth from growthcraft to 1 to limit exponential growth. Also, make sure that any method used to auto-harvest them will be suitably gated behind expensive and obnoxiously created machines.
This keeps Botania from being Day One And Done, it requires you to spend a significant amount of time cross-breeding the flowers, and requires the specific soil that you can require certain ingredients to ensure that they will be gated behind this at least.
* Any 'passive' plant requires diamond dust as a component in the recipe to create.
* Flat across the board reduction in mana output, say 10%, and flat across the board increase in mana requirements for just about everything. You can claim the reduction in mana output isn't really a reduction in output, it is energy inefficiency. No energy storage device is 100% efficient, that breaks the laws of thermodynamics as we currently understand them. So have some 'energy loss' inherent in the system. In fact, I'd almost say, if it were possible, that for every ten points of mana the Mana Spreader only emits 8 or so, just to give you some kind of energy loss. Maybe a basic only emits 7, the elvin tech emits 8 and the gaia spirit tech emits 9, giving you more than just throughput as a reason to upgrade. Same concept with the mana pools. For every 10 points of energy stored, you can draw only 7, with the last three lost in the energy exchange.
* Increase the cost of materials required for runes. Have them all require some sort of silk-touch material (earth requires coal ore instead of coal block, etc...) to gate runes behind silk touch.
* Set up some sort of resource bleed system. Maybe flowers require petals or fertilizer every so often to 'repair' them, maybe mana pools lose durability when they gain or lose mana and need to be repaired periodically or they start 'leaking' and finally stop functioning. Maybe you have to replace the lens in the mana spreader every so often.