I was after something similar myself but was told that Google flights and the ITA Matrix are the best options, Flights works very similar to Matrix, it still takes multiple searches of airports but doing 5-6 at a time.

The main problem I found was that it would not find the correct fares for CX, QR or SQ many times (Flights and ITA were giving me flights more expensive than what the airlines were actually offering) , even with specific searches from single origin and for that AFAIK there is no alternative than looking individually either on Kayak or similar or Airline website.