Is this taking over the galaxy or just a battle of decimation? If the former I'm not sure because the reapers could possibly indoctrinate the flood gravemind and rule the galaxy that way. If a battle of decimation I would say the reapers because if they really wanted too they could eliminate planets on whims. But I would also say these are two very different forces and I think it would be a better question to ask which force would be harder a hero to eliminate.
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