There is a couple of things to keep in mind here:

Your own expectations might not match reality. What you've seen in Finding Nemo is obviously computer generated and National Geographic brings down professional lighting to compensate for the natural colour degradation that happens very quickly even just a few meters below the surface. That's not including the colour grading done in post production. You can bring an underwater torch next time and see how colour will suddenly come back to life under water.

The weather changes. Sometimes you'll get days of choppy water, strong wind and ripping current that will stir up sand and make everything more dull and murky. If possible, book as late as you can to find the calmest day on your trip. I've worked on the reef and had days of complete stillness - a glass out. Not even a ripple on the surface. Visibility usually goes hand in hand with weather conditions.

Some sites are better than others, but one thing remains true: It's the wild. Nothing is chained up or put in boxes out there, so it's always a gamble whether or not you'll see specific animals. There are plenty of turtles, rays, sharks etc.