I'm in the camp that thinks would pretty much naff up the local ecology. Pyramids of biomass and all that - one whale eats a thousand fish, those fish eat a tonne of plankton, etc. I don't understand why reducing shark and whale populations is considered a good thing given that there are so many people out there trying to increase those populations to combat the result of hunting, water pollution and so on.
The main issue here is human intervention has had an impact on fish populations anyway what with trawlers and the like, and to get even more involved would probably result in more drastic knock-on effects.
If you take the humans out of the equation, nature's been running its course for thousands of years with no problem, and no cages.
I'll admit to not knowing a great deal about fish habits, but I wouldn't have thought it was in a lot of aquatic species' nature (or intelligence) to know to set up a home within the confines of a cage. And as has been mentioned at various points, predators could also be candidates for living in the cage, therefore making it easy pickings for them.
A different (possibly better?) solution, I think, would be to set up a barrier, rather than a cage. If fish are on the run, they'll dart through a mesh barrier, whereas larger predators would be stopped by it. But again, I don't see why this needs to be done.
My own personal opinion - no good ever comes from playing God with any species, and I don't think this will be an exception.