hoping to get two greenhouses in a week. I've been wanting to get into aquaponics for a long time.
When it comes to the fish, everywhere I've looked, the focus is a monoculture approach. Why not create a habitat and raise fish-guilds + aquatic plant guilds. Has anybody ever heard of applying the idea of guilds to aquaponics?
Not in aquaponics, but in aquarium scale fishkeeping it is known as a "community tank". This can be rather challenging, as a great proportion of fish are opportunistic piscivores, eating any other fish that they can. Tilapia are herbivores, but catfish, another fairly common aquaponics choice, are definitely fish eaters, so, for example, you would not want to keep catfish with tilapia.
Stocking densities in aquaponics are routinely high, so your herbivorous tilapia would make short work of aquatic plants grown in the same space with them.
On a distributed basis, with fish in one tank, then plants in grow beds and/or their own tank for aquatics, and possibly crayfish under growbeds, well, that is the idea of aquaponics
Essentially, the answer to why not do fish and plant guilds is that at productive densities the fish will destroy the plants and each other. Tilapia being herbivores are not going to eat one another, but I bet that in catfish aquaponics there are losses to cannibalism.