I would also recommend staying in the Low Countries. You will spend enough time on planes to and from Malaysia. In the Netherlands, I believe two days for Amsterdam would be the minimum, and I'd recommend getting out to either Haarlem, Alkmaar, Zaandam (Zaanse Schans) or further to The Hague, Leiden, Delft, Rotterdam, Utrecht, s'Hertogenbosch to get a broader taste of the Netherlands, according to what you will find most interesting.
I also agree you might want to spread out your time in Belgium between more than just Brussels. I believe staying in Antwerp you reasonably well-connected to the rest of Belgium:
1. The Intercity trains from the Netherlands to Belgium as well as the Thalys stop in Antwerp
2. There are direct trains from Antwerp to Ghent, Brugge and Brussels
3. There are direct connections to both Schiphol (Amsterdam Airport) and Zaventem (Brussels Airport)
There are also hotels at reasonable places to be found very close to the central station in Antwerp.
Edited: 4:43 pm, March 16, 2013