The old idea of botanical and zoological gardens is a collection of exotic species to show them at home and carry out further research.
Don’t build collections anymore, build ecosystems!
It is not very difficult to realize the connections between species and make them the central message. Many botanical and zoological gardens have already begun to do that by allowing animals in greenhouses or having plants in animal compounds. It can be much more interesting for visitors to realize and watch all the different actions going on, than just one or a few species in a cage without interaction.
A further idea: Show all the levels of evolution, including bacteria and fungi. The categories “plants” and “animals” alone are a little outdated, since we know now, how much richer life on Earth is. Some bacteria and fungi can glow in the dark for instance and have other nicely to watch traits. Mushrooms might not be visible all the time, but they can be included. And it might be possible to build and install large binocular microscopes to watch small or microscopic lifeforms conveniently, or maybe on a screen.