On the face of it, I really like the idea of aquaponics too. We feed fish which produce waste that feeds plant. The plants clean up the water which goes back to the fish. And then around and around we go.
The drawbacks I see, though, are:
* If it is too intensive it resembles a shed full of caged chickens. I'm sure a "caged" fish will be as happy as a caged chicken, NOT!
* Fish food is generally full of grain and/or soy. Feed fish an unnatural diet consisting of heaps of grain and you will get the same old problem, o6:o3 ratio out of whack.
* Getting set up CAN involve a big investment. Aquaponics seems hot right now so of course there are heaps of experts flogging, ebooks, DVD's and full blown system ranging from several to tens of thousands.
* Temperature sensitivity of certain fish species and or veges.
* Systems can run out of nutrients that the plants needs that don't come from the nitrogen cycle that is looked after by the fish and plants.
However as I am very keen on setting up a small backyard system I have tried to overcome these issues:
* Don't overstock your fish tank. I've seen various fish stocking densities ranging from as low max of 17 kg/m3 (kilogram to a cubic meter of water) to 25kg/m3 all the way up to 40kg/m3 as a max. As a guess I would think 40kg/m3 is your caged chicken stocking density, 25kg/m3 is your barn raised chicken and under 17 (much lower) may be free range. Well technically free range would be farming from a lake or dam that has its own evosystem.
* Pay a little extra for biologically appropriate fish fod without grain or soy. Even better incorporate a feed producing system into your urban farm, ie worm/soldier fly larvae farm, duck weed pond, etc.
* Use your noggin and design a system from recycled/re-purposed materials that are food safe and locally available, ie IBC's (Intermediate Bulk Containers) and 55 gallon barrels.
* Grow fish and veges that grow locally. That way you avoid heating/cooling costs of water and greenhouses/grow beds.
That was a little long winded. I have been over thinking aquaponics for a while now. So my answer is aquaponics with a sustainable, environmentally approach. And Polyface. Those guys are great :)