Er, wading through this thread is a little intense (about 2+ years of notes, right?). How about perhaps re-starting it or at least summarizing the main points somewhere?
As to fish suggestions, being mainly a Caribbean diver, I'd like to see more Caribbean species, of course. Sargeant Majors would be neat as would blue chromis, and... well, all of Paul Humann's Caribbean book
s (gotta include the invertabrates and corals, of course) would nice, please.
A couple of details which, I suspect, are easier to ask for than to complete but... 1) a small amount of "whale snot" (general floating debris) in the water would help give a better illusion of depth of field; 2) even in a relatively shallow (i.e., "front to back", not "top to bottom") tank, fish further from the viewer are ever so slightly faded compared to closer fish, adding this effect would also help with the illusion of depth.
Someone touched on the bubble sound being repetitive. IMHO it's pretty good at avoiding repetition unless you listen closely but... perhaps mixing multiple bubble tracks so the "seams", where they repeat, don't always match up predictably would help here. The brain is pretty good at picking out patterns (even where they don't really exist); enhanced randomness in the sound track is the goal here.
Finally, beware of the truck-sized Swiss Army knife! I worked with a group that developed an astronomical image enhancement program (Registax - uses wavlet processing - ask me about it off-list, pls) and the greatest challenge was avoiding adding so many features (hence the term "truck-sized Swiss Army knife") the program would only run on the biggest and fastest of PC's.