The thing about se asia is there is it depends which cities you want to go to.
Singapore / Malaysia would be better to indonesia than say Thailand, but Thailand would be better for vietnam cambodia etc, but seriously depends on where you want to go.
I believe that starting in Singapore and ending in Thailand or vice versa with an open jaw ticket (if that is possible) would be the way I would do it.
However, if you want to use 1 city as a hub and:
1) travel budget carriers - Singapore is the main hubs for budget carriers.
2) earn SM & MQM - vietnam airlines
3) only earn SM - malaysian airlines