Let's see... The only generating flowers i can think of that NEED babysitting are the thermalily and the rosa arcana, possibly the dandelifon. Maybe the passives if you really want to use them on more than entry-stepping stone.
Endoflame: Extremely easy to automate, item dropper + pressure plate or timer or a setup that'd work with a gourmy/entropiny
Munchdew: Set it up near a tree farm so it doesn't eat all the leaves and thus leaves enough saplings for the tree farm to sustain itself.
Gourmaryliss: Timer based item dropper, or use a system based on mana flow.
Entropinnyium: Use a system based on the mana detector, when mana stops flowing and there's room in the pool, set off TNT.
Kekimus: The challenge here is more on making the cake. Placing it is easy.
Spectrolous: Gathering the wool is pretty easy (use a sheep farm with 16 different coloured sheep). The challenge is dropping the wool in the right order if you automate.
Rafflowisa: Like the Kekimus, the challenge is making the Passive flowers for this to munch.
Dandelifion: This is the one flower (other than raffl) i haven't made an attempt at automating. But I can see it being automatable.