Since this thread has risen from the dead.. and that now I'm actually getting deeper into Botania (I've made my portal, but haven't powered it yet), I do have some feedback.
I don't totally agree that passive flowers should "decay". It's clear to me that the default is way too low. As stated, you either skip from daybloom/nightshade as quickly as possible and never look back, or you tweak the config to ignore decay.
I use a small patch of dayblooms to feed my Jaded Amaranthus and Hopperhock
I use a small batch of Nightshades to feed mana into a pool I use only for creating mana versions of things (petals, pearls, diamonds, manasteel).
To have to keep going back in there and re-making and replanting the 8 or so flowers of each is mind numbing.
Maybe, make it so the passive flowers can only transfer mana to a "low tier" spreader, that can only shoot into the first tier mana pool, and make the first tier mana pool unrecognizable to sparks. This would restrict their "abuse", and still give those flowers a meaning beyond "Day 1".
I also agree, that the systems we have to make to "feed" mana producing flowers are.. ugly. I LOVE (yes all caps) the Hovering Hourglass! A great addition! Thing is, it needs a redstone torch to "invert" the signal. Could we maybe add some redstone to the Hourglass to make it so it is always producing a signal (like a redstone torch), and only stops when it is turning? (Opposite of how it works now)
Hopperhocks are great at grabbing everything, and I like the addition to tell it to ignore items in frames attached to the chest it feeds into, but I agree, there needs to be some kind of item transport as well. I like the idea of "cannon flowers" (hello Plants vs Zombies). A Hopperhock, set to a chest, a "cannon" set to that chest aimed at another Hopperhock, set to a chest... Well, you get the idea
I wouldn't even ask for it to actually show the item being shot through the air, just a coloured mana burst to indicate it's working...
That's all I have for now, except to say I'm really enjoying Botania. The only other mod I've touched in this play through on my server is MFR for a tree/charcoal farm (to feed my flowers) and ore doubling...
Keep up the great work!