I'm also pretty down on Malaysia as a country due to the racism directed by their government (generally anti-Chinese/pro-Malay), which seriously influences economic policies -- both in their goals, and their general desire for a top-down centrally imposed plan for things. This sort of works in natural resource extraction, but is antithetical to startups. I'd probably bet on Indonesia instead of Malaysia long term for this reason; less state-directed, more chaotic and natural.
I can't speak for Malaysia, but agreed on Indonesia. I just visited a co-working space, Jogja Digital Valley (Yogyakarta), and got the feeling that good things would come of it. It will take time, but the combination of skills (Gadjha Mada and many other universities) and capital are here (8 companies get around 30k which goes much further here). The main problem with Indonesia is their poor Internet connectivity, unless something is done, it seems hard to imagine a Facebook being born in a dorm room or garage.
Yogyakarta was great when I visited in November -- it's got a lot of universities. I didn't know about the coworking spaces.
The "dark horse" for SEA is Myanmar; assuming the elections go well in 2014/2015, I could see them turning into a great place with essentially greenfield infrastructure investments over the next 5-10y.
This is hugely important. So many places have tried to copy Silicon Valley, but it's just not very easy to artificially put everything together.