The lack of empathy simply comes from the representation BioWare chose for the Geth: apart from Legion – the only platform designed for independent operation, all Geth are swarm-like non-individuals. They don’t have identity, so why would I feel bad about them?

The depiction of the Reapers is a lot more interesting: each Reaper is a nation, but the whole nation can be addressed as an individual. This is something we understand at the end of ME2, when we see the Reaper fleet creeping toward the galaxy: each Reaper has structural differences, reinforcing the idea that each of them is an independent entity.

Now of course, BioWare needed cannon fodder for the game, but in a way, it’s too bad that the ant-like species is the one we encounter during gameplay.