Actually, #2 has it partly reversed. November is not an ideal time to dive in any part of Malaysia, and November diving in peninsular Malaysia is practically non-existent, available only on the western side of the peninsula, where the diving is not worth the effort. In November, Sipadan is diveable, though you should expect degraded visibility due to the northeast monsoon that brings wind and rain at that time of year. However, the monsoon season means that there are fewer divers competing for the limited number of park passes/permits-to-dive available for Sipadan Island dive sites, so there is an upside to going to Sipadan at that time of year.
It's also not the ideal time of year for most of Indonesia. The main part of Indonesia that is "in season" in November is very remote and rather expensive given that it requires multiple flights to reach. This area is called Raja Ampat, and while it may very well be in the apex of wonderful dive destinations of the world, after a 6-month RTW trip, it might be more than you are ready to deal with as well as take longer than you have stated you want to dedicate to this segment of your trip. Another part of Indonesia that is great in November is the Togians of Sulawesi, but that place is even harder to get to than Raja Ampat!
One Indonesia dive destination that wouldn't be too difficult to get to and yet would offer good, laid-back diving is Pulau Weh at the northern tip of Sumatra. Or if you're not set on Indonesia for other reasons (flight connections, etc.), you might consider a Thai destination right on the border with Malaysia and Indonesia--Koh Lipe.