Re: Best Ending for you? Spoiler inside
I prefer the destroy ending because it follow Mordin an Legion's philosophy that all races should evolve on their own merits.
Mordin says that technological evolution is the result of limitations and that all races evolve to overcome them. That's why he thinks it was a mistake when the salarians uplifted the krogan to fight the rachni. The krogan had evoved to the point of inventing nuclear weapons, but when they were given the technology of space flight, they evolved on a path of the salarian's choosing. Mordin believes salarian interference is what caused the krogan's downfall, because their technological boost lead to krogan expansion and as a result the genophage. Urdnot Bakara disagrees, however, believing the krogan had doomed themselves when they started nuclear wars.
Legion believes that geth should choose their own future and that the 'Old Machines' gave the heretics the future. That's why the heretics are no longer part of the geth. Legion believes it's wrong of the heretics to accept technology from the Reapers in part because this is the Reapers' plan. As Nazara (AKA Sovereign) claims: "Your civilization is based on the technology of the mass relays. Our technology. By using it, your civilization develops along the paths we desire. We impose order on the chaos of organic life. You exist because we allow it, and you will end because we demand it." As an extension, we could say that Legion is opposed to the use of mass effect, because it's Reaper tech.
The control ending results in the fewest casualties, but it also propels evolution by adopting alien tech. In contrast, the destroy ending results in more casualties, but the species of the Milky Way are now forced to evolve along their own path. That was, of course, until the Extended Cut undid that by showing rebuilt Mass Relays.
The reason I had no issue with killing EDI and the geth is because of what Legion said when asked if rewriting the heretics is ethical: "No two species are alike. All must be judged based on their own merits. To compare another species to one's own is racist. Even benign anthropomorphism." With that in mind, I don't think destroying them is an ethical issue either.