For a different approach to diving these islands --
At the end of October I spent about a week staying in Semporna and diving Sipadan, Mabul, Kapalai, and Sibuan with in-town operators. I showed up without advance plans, except a couple of nights booked at the Sea Fest Hotel, overlooking the fishing boat's dock site. There were real pros and cons to this approach:
The Pros: (1.) The local dive operators I used(Borneo Speedy Dive and Uncle Changs) had Sipadan permits immediately available for 2 day packages or even no package at Speedy Dive. Scuba Junky, by contrast, had no Sipadan permits available for two weeks. Speedy Dive however gave no credit for providing your own gear and charged 1200 ringetts for one day at Sipadan but only 1300 ringetts for 2 days of diving, including three tanks at another island, which varied by day. So of 6 days diving I spent 3 days at Sipadan and 1 day each at Mabul, Kapalai, and Sibuan(by far the worst diving. Choose one of the other islands). (2)This approach is much cheaper than the offshore resorts, even though Sea Fest was a relatively expensive onshore hotel.
(3) Much more exposure to what local life is like, particularly if you walk off peninsula into some of the waterfront neighborhoods, if local life interests you.
The Cons: (1) Dives generally limited to about 45 minutes and I am assume dive guides at the high-end resorts have better knowledge of local marine organisms (2) Though the scenery on the daily commute to the islands was interesting, after a few days it got old and time-consuming and if you hit bad weather it would be very uncomfortable. (3) This approach will not work during the high tourist seasons.