I've been SCUBA diving in KotaKina Balu. It was my intent to go to Sipidan, but couldn't make it, so I stayed in KKB. I'm looking at a return trip to Malaysia for some more diving, but also want an area with some eco-touring, without returning to northern Borneo. Does anyone have any knowledge of where in Malaysia that has good eco-tourism and SCUBA? I will also consider Brunei.
I suggest the Perhentian Islands. It's off the east coast of west Malaysia (so not Borneo) and is relatively less frequented by tourists. Access is easy from the town of Kota Bharu - part of the Jungle Railway route - from where it takes 1.5 hours by taxi (or slightly longer by public bus) to reach Kuala Besut. A speedboat ride should cost about 60 MYR and take you in an hour to wherever you want to be dropped off on the islands.
Had you try Tioman Island? It's located at Southern part of West Malaysia.
Though honestly, none of the dive sites in peninsular Malaysia are even remotely close to the mindblowing beauty of Sipadan. Then some eco-tourism on the Kinabatangan river (saw live wild Orang Oetang there) and there really is no reason not to go back to the Eastern tip of Borneo.
If you really prefer peninsular Malaysia, the east side has better diving. Tioman and Perhentian are the two most famous spots.