The Hanging Tree / Bulbo Tree is much to easy to get. Since I know where it is, there is no use for any other food or water source anymore. That makes the game too easy once you know it.
The solution is to make farming much less efficient - so it is still easier to hunt. I estimate that having plants grow at about 1/50th the rate would make it about as inconvenient (requiring dedicating an entire level of a base to farming). If you want to undermine farming more, then the solution would be to make it even slower (say eighty times slower). It'd still be a cool late-game feature, but only larger bases would be self-sustaining!
Or just force farming to use base energy (light and heat for the plants) and water sources (need a water filtration machine diverted to plants). A tree with reach fruits might not look so good if it needs lots of water and energy.
A plant with less rich fruits might need less energy and water and thus be better to farm.
But you're right with hiding good plants. Better would be to only find an example inside a deep precursor base. Maybe from a time where those plants existed before they got extinct. The precursors have captured a last example in their greenhouse at their bases. Once you find them, you get access to far more rich farming plants than on the floating isle.
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A plant with less rich fruits might need less energy and water and thus be better to farm.