An interesting question.
I was in Papua last Jun. Some of the dives were amazing so many fish.
I found the fish life to be similar to the Maldives(in terms of quantity, not number of differnet types). Reefs/corals in RA are the best i have seen. There is also lots of small stuff. The passage & mangroves were also amazing. There is also a fantastic manta dive.
Now for cons - It can be expensive, it is definately a pain to get there, malaria is a concern & i stayed in a basic resort with basic facilities. however it is definately worth visiting once, especially if you are based in Singapore.! I also had very high expectations and was a little dissapointed a couple of days. It was rainy and quite gloomy underwater.
Compared to Sipidan the travelling time is probabily similar, as Sipidan is also not easy to get to. Sipidan is nice(you can have amazing dives there if you get lucky) but there are a lot more divers & the permit situation is not great,it is also expensive. Definately go RA rather than Sipadan.
Bunaken is nice, easy to get to , many nice resorts & can be cheap but should not be compared to RA.
I say go RA but keep your expectations in check & build some flexibility into your travel plans.