I should make clear about my post on SEA diving. Sipadan's big schools are "memory for many" but they still do occur, just "not seen all that often". For a lot of time, they usually stay in smaller schools of 00s.
As for the whaleshark sightings comment, Lankayan ( for Scren who must've gone to their website) claims whalesharks visit them regularly in March. It was a 1 time occurrence as was Mataking.
Zippsy re: Ambon: yes there is still some muslim vs christian unrest on the island. But how does that affect a liveaboard diving in the pinnacles offshore? That said, you'd be hardpressed to find a liveaboard crew who will go near Ambon. Many of the indonesia liveaboard crew are Ambonese and WILL NOT go near ambon. They'd rather mutiny. There are 1 or 2 boats who'd do it. As for security for Americans in Indo: I have this to say: There is a relatively large american expat population in Bali ( I being one of them, when I'm there) who live quite happily and safely. If anyone is concerned about their safety, then they should avoid the area. No one should go on holiday and have to worry about being bombed, kidnapped or anything else bad unless of course they are naturally worry-warts
The active words are risk aversion factor and perceived risk vs actual risk.
Frogfish: I personally would not spend money going to Wakatobi the resort. Their diving practices, accomodations, facilities and food are not worth the money. Better to go by liveaboard to Tukang Besi Islands and the Take Bone Rate archipelago. It's very easy to run from Komodo to Tukang Besi from Labuhan Bajo.
Comparing Sipadan and Bunaken, you also have to look at the larger picture. Doing Bunaken alone, during Sept - Dec, you have a very small chance to see Sperm whales or orcas, but they are there. There are sites in nearby Bangka Islands which rival the macro of Mabul. The soft corals of Bangka Island are much better than anything Sipadan has to offer. But Sipadan definitely has the bigger schools of fish and of course the turtles.
I compare Sangalaki to Sipadan because of their proximity to each other and also the similarities. Of course Sangalaki has the jelly fish lake and super lagoon drift dives like Palau and the mantas like Yap as well as nice caverns (vs turtle cave in Sipadan)
Scren, decide what type of diving you like. Pelagics are better had elsewhere than the Indo Pacific area. Indiscriminate fishing has wiped out a lot of areas. Since you want to do land based activities, then Sabah would suit your needs nicely. Zippsy mentioned a few things, Sepilok Orangutan reserve, the probis monkeys off Sempoerna and of course the islands are all wonderful.
As would doing Komodo and then relaxing in Bali and their numerous spas, a short flight to Borobudur for a wonderful day of temples (and definitely run to the Sheraton jogjarkarta for a break at the spa). There are numerous treks to be done in Lombok (trekking up Rimjani) as well. Then you can dive the Nusa Islands for Mola Mola(Sunfish too).
I'd do them all (and I have)
