When the Imagineers were designing the Submarine Voyage, it was planned to have real fish swimming about. The plan remained that even after the initial track and submarines were built and put into the lagoon. This is why you see bubbles before and after the loading station, because it was determined by experts that the fish would get trapped inbetween a submarine and the loading station, and die. However, Walt scrapped the plan because at the time they were building it, (with borrowed money from the bank), they woudlnt be able to afford constantly replacing dead fish
So the current plan with the Submarine lagoon is to put in "finding nemo". we can all complain about how incredibly stupid the idea of it is, but the bottom line is that it is good thing the subs will come back in some form.
But why does it have to be in this form?
Why couldnt they install these "plastic boxes", and instead of putting an animatronic 'nemo' in the box, why dont they put REAL FISH? Make it (somehow i dont know) accessible underground so you could feed them, or make it so divers could access them underwater, put fish food in a little box, which after it is closed it sucks all of the food and shoots it in the box full of fish.
Just put real fish in the water. Dont use chlorine, just use some other chemical that is fish-friendly that could help keep the water clean. If the ocean waters in tropical areas such as Hawaii are so clear (They have a REAL submarine there that takes tourists to see stuff chillin' on the ocean floor), why cant they just use real fish? Maybe even put a bunch of clown fish in so you could truely 'find nemo'