I was also a bit disappointed with this. Another is the Great Barrier Reef. I guess one main thing with everyone's disappointments is due to high expectations.

I had seen some corals near India's Andaman islands which were very colorful. So when I saw the Reef's bland colors, I was disappointed. However if I was to go there again, I would do the sea walk thing. They take you in a boat a little far from the island and you get into a divers suit and climb a ladder down to the ocean bed. You then walk on the ocean bed holding some railings. That is something I have always wanted to do.