That's interesting. This was my first trip to Sipadan so I have no basis for comparision. I did see some trash in the water on the boat rides from Mabul to Sipadan and once during a dive at Sipadan, not anywhere near as much as Lembeh Straight. The vis at Sipadan was poor for a tropical place. It's their rainy season and I was told they had lots of rain the week before I arrived. I was lucky that all but one of my day dives were sunny. I did not see many large schools of fish, the jacks that I got a few photo of was the only encounter. I asked the guide about the schooling barracudas, and was told that they haven't seen them in a month. We did see lots and lots of large turtles: some of biggest I've ever seen.
The macro life at Mabul was wonderful, but the vis here is even worst.
I'm afraid my observations are a little biased because I had the good fortune of having Klaus E Fiedler, the author of many of the fish guides as my dive buddy for the week, and he told me in stronger language about the decline in the marine life. Ms Carret, the writer cited in the article was also at the same resort with us and I listened in on some of the conversations between the two about this topic. Klaus is now back in Germany, keep a watch on German publications for his article about Sipadan and also Russian divers.