My view on the ending morality

The writers, aka the Catalyst, decided to say "fuck you" to the player and gave us three horrible choices: You won, but we're forcing you to win our way. One does not simply slay the dragon and walk off into the sunset. But the morals in the game are bigger than just the ending. In ME1 it was more straight forward. When the story for ME1 was written heroes were still allowed. The same in ME2, but they threw Arrival into that one so you could learn what it felt like to be a monster.

If you were a completionist, there is a side quest in ME1 you could stumble upon where you found a derelict ship that returned from Geth Space and the entire crew had been turned into husks. The nav logs indicated that this was a message from the Geth that this was what happens to organics who intrude on their territory. Tali also needed something from Geth that were not influenced by Sovereign. We learned that the Geth not influenced by Sovereign were planning an invasion from the Armstrong Cluster. That was her ME1 pilgrimage mission. This indicated to me that the direction of the writers was to have the Geth continue to be hostile to organics throughout the series regardless of the reapers.

Legion or Not Legion showed us clips of the Geth side of the Morning War. What happened with the Quarians is that the Geth started behaving in ways they were not designed. They were considered to be smart appliances. They got too smart and refused shutdown commands and thus people were given instructions from the manufacturers to do hard shutdowns. The Geth rebelled. You have to remember that they were still considered to be appliances. And then the war started. I would imagine all synthetic rebellions throughout galactic history were like this. Even our own someday will be like this should we be idiotic enough to build sentient AI.

So in ME3 the Quarians developed a weapon that allowed them to weaken the Geth enough to take reduce their number to the point where they could defeat them and take back their homeworld. The Quarian ships had about 80 years of life left in them before they needed to settle on a world anyway, and the Council wasn't having any of that. But plans went awry when the reapers invaded and took over the Geth. The idea of the Reapers was to keep both of them occupied in a stalemate until both could be harvested.

Refusal was never an ending in the original game. It was added because a number of people complained that they didn't want to choose any of the three endings, so the writers gave them the "rocks fall, everyone dies" ending. Also there was the fact that many of us just stood there and shot the Catalyst for lols. 

Through the series starting in ME2 you begin making decisions that are morally reprehensible:

• If you do Arrival, you kill 300,000. If you don't do Arrival you lose 50 War Assets because Hackett sends in the Marines to do the job. Shepard is arrested for working for Cerberus.
  
• If you do Legion's loyalty mission, you have the choice of killing a ton of Geth by blowing up their server, or killing a ton of Geth by rewriting them.
• If you sell Legion to Cerberus in ME2, you can't make peace between the Quarians and Geth in ME3, plus the Geth are stronger.
• If you or Ashley killed Wrex in ME1, you're headed down a dark path - save Maelon's data in ME2; fake the Genophage cure and send Mordin to work on the Crucible which dooms the Krogan after the war.

The only way out of what I call "Walters' Box" is to not have Legion in ME3. It's metagaming. That leaves you with the Geth VI or "Not Legion" in ME3 where you can't make peace and you choose to "let the Geth die" which is on Gerrel's hands, not yours. Your other choice is to "let the Quarians die" and you get to watch Tali commit suicide. Why the idea of uploading "Reaper Code" to the Geth is a good idea is beyond me. We're supposed to take Legion's word that Reaper Code is fine when we've seen Reaper tech indoctrinate everything it touches. But the feelz. 

I think this is probably the least monstrous play through of the game:

• ME1 - Save the Rachni Queen
• ME1 - Get Wrex's family armor and resolve the situation on Virmire - you don't even need the "I win" dialogue because he's your friend.
• ME1 - Do the Armstrong Cluster and do Tali's pilgrimage
• ME1 - Save the Council
• ME1 - Let Balak live - you can leave him for the Alliance or let him escape outright. It doesn't matter. If you let him escape outright you save the hostages.
• ME2 - Save Maelon's data
• ME2 - Sell Legion to Cerberus - it was a non-functional machine at this point, and this gets you out of killing or rewriting millions of Geth but it will cost you war assets in ME3
• ME2 - Don't do Arrival
• ME3 - Cure the Genophage
• ME3 - Priority Rannoch - side with the Quarians because you can't make peace and Geth VI doesn't trust organics. The deaths of the Geth are on Gerrel's hands.

You actively prevented the geth from uploading the Reaper code. You can not claim that the Geth's destruction is on the hands of another when you directly effected it. You are basically trying to claim you didn't kill the person the bus driver did. All you did was push them out in front of the buss.

After the reapers have been destroyed, the galaxy won't give a crap about the geth going bye, bye because had the reapers not been destroyed the rest of the galaxy would have been harvested.

"Human nature." Always improving by the exchange of ideas though. Never perfected. That's life.

Even with Legion present and being able to establish a peace, I don't see allowing the upload as best choice without meta-gaming.

The Geth in ME3 are not the same Geth of ME1, ME2 and the novels written by ME1's lead writer. They were written in ME3 to be sympathetic to the player as victims, and vilify the Quarians to better fit the narrative ME3's writing team wanted to tell. Ignoring that, it is easy to reason that Legion was altered in the time the Reapers were using it as a transmitter. In ME1&2, and the novels the Geth are isolationist murder-bots, who kill any organic that ventures into the Perseus Veil, no questions asked. They even killed Quarians who attempted to negotiate a peace with them, something ME3 ignores and leads the player to believe the Geth were caring for Rannoch in the event that the Quarians would one day return when peace was established. In ME2 Legion talks about how the "true" Geth want to evolve without the influence of the Reapers, only to change its stance after being exposed to Reaper code in ME3. Legion/not-Legion gives a very one sided portrayal of the Morning War, and changing the video logs so that it is "easier" for Shepard to understand. Would have seeing the Quarians without their suits caused Shepard to have sympathy for current day Quarians, when Legion/not-Legion was regaling Shepard with the "true" history of the Geth's distress and the Morning War? First time through ME3, I honestly thought allowing Legion to upload the code would come back to bite Shepard. Sarcasm:I mean it isn't like Legion deceived Shepard twice during the Rannoch story arc.

In regards to the ending I agree with FiendishlyInventive . I could list other arguments against control and synthesis, but those have been discussed previously numerous times over the years.

They are still fully sapient and independent at this point.  Simple VI wouldn't be able to ask metaphysical questions and even stray into religious worship. They would not be able to take stock of their own morality and react accordingly, even if it is ultimately a bad choice they made.

But ignoring the fact that at the time of the upload the Geth are no longer capable of that. Their unique intelligence so diminished that they are no longer capable of sapience.

Legion mentions that the way the Geth gain intelligence and sapience is by networking together, alone and in small numbers they are a simple runtime or program. In their initial attack the Quarians wipe out a large number of Geth programs, lowering the Geth's intelligence to the point where the Geth fear losing sapience and turn to the Reapers. By the time Shepard and crew take out the Reaper and even more Geth, there are so few Geth remaining they don't have the intelligence to mount a defense. The Geth are at the point where they are just a collection of runtimes not an AI, spread out among ships and mobile platforms. Hence why Legion/Not-Legion is in a rush to upload the Reaper code.

The Quarians have largely succeeded in defeating the Geth, the uniqueness that made them Geth has been destroyed. Allowing Legion/Not-Legion to upload the Reaper code isn't so much as saving the Geth as it is giving rise to a new form of sentient AI based on Reaper code.