Something Legion said to me when I talked with him about the Geth actually influenced my decision concerning the fate of the Collector base in the endgame. By inclination, I would be sorely tempted considering how terrifying Reapers are to agree with TIM and EMP the place to salvage tech from it. Legion, however, said earlier that one error of the "heretic" Geth is that they are relying on Reaper tech to develop instead of following their own path. He also reminded me of what Sovereign said back in ME:1... that by using the Relays and the Citadel , organic life develops along the lines that the Reapers want. Our dependence on Reaper tech is perhaps their greatest weapon against us.
Examples:
- The Citadel is a huge Reaper ME Relay.
- Reapers can directly control cybernetic organisms with Reaper-tech installed: Saren, Harbinger.
- The IFF drive virus.
- Using Sovereign as a ship...Indoctrination.
- Reaper instigation of the Rachni War.
I think Legion is on to something. The Reapers are terrified of the unpredictable. They have been using organic civilizations as a means of reproduction for eons. If we, predictably, try and use their tech against them, they still have some control over how we develop or try to challenge them.
That said, I thought it was a little out of character for Legion (who was in my team after I took the Reaper down) to present the choice as morally neutral.