A bunch of things could have been done to make passive flowers more inconvenient for mass mana generation.
Requiring a clear view of the sky would prevent hydrangea stacks.
Getting them to use sugar cane semantics and require water directly adjacent to their root level would make them a damn sight more attractive, as well as more inconvenient to stack. (Same applies to the lava eating flowers - root level please!)
That is all, because all the "I have too much mana to move from passive flowers" really seems to revolve around hydrangea stacks.
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PS. Someone from the 'i love to automate botania' camp please post some screenshots of a build where flowers are automated, but the flower is on the surface, and the automation is hidden underground. The 3x3 area around the flower should be flat grass.
I hate automating stuff, so no screenies, sorry.
But just because I hate something, doesn't mean I want it gone.
Imagine how quick Thaumcraft would be to get the end game stuff if you didn't have to scan (which I believe SHOULD go) and research stuff (which SHOULD stay)
As for the hyrdos. I agree on the "root level" (level above the water) as it would look a damn sight nicer. However, it wouldn't have balanced them in any way, shape, or form. And hydros aren't meant to see the sky, although I get where you are coming from, I don't think that is a change people would take kindly to either.
Dayblooms and nightshades are supposed to be the only 2, to my knowledge, that require a sky view. After that you are free to have all your flowers hidden underground.
Back when Botania first came out, unless I am mistaken, you could have dayblooms (I will just use the one) next to each other and they would still generate the same amount of mana. However, people abused that, and spammed them. So vazkii nerfed them, by saying they couldn't be next to each other. Did that dissuade people? No. So she lowered how much mana they gave. People still used them, but used more of them.
After nerfing, and nerfing, trying to get people to stop using them* she probably just said "the easiest way to stop their use would be to remove them" and came to the conclusion that withering was the only option.
*She wanted people to stop using them as she got multiple "bug reports" complaining that they (the people using the mod) couldn't do X with passives. Or that they weren't making enough mana with passives. Or some saying things like "I have 100 dayblooms, but it still takes ages to create enough mana to Z"