*WARNING. MAJOR SPOILERS AHEAD. READ AT OWN RISK.*
I have created the Poll as well for people who merely want to chime in a quick opinion, but the option is, of course, open to those that participate in the discussion below.
Fallout 4 has shown to be a very morally questioning game in general. As apposed to Skyrim, where you could pick one side out of 2, you have the option for 3, and all of them have long term goals in mind, and all aren't necessarily 'evil' by the direct definition due to their backgrounds, but also have major flaws in their ideals, and all of them revolve around a specific character race, called Synths, specifically Gen 3 ones.
Synths are machines created by The Institute that look, sound, interact, and behave exactly like a human would, or at least the Gen 3 versions do. The Gen 1 and 2 versions are considered "dumber", and are used by The Institute in their fieldwork, mind you. The occasional Gen 3 is employed for other tasks such as infiltration.
But here is where the Moral Question is popped. Gen 3 Synths are so smart, and are so near free will, combined with free thinking, are they considered people too? Numerous times throughout the game you will see Synths act 100% like a human would, no fakeness (unless on purpose) is shown.
The Brotherhood of Steel wishes to preserve technology and save humanity from itself by gathering technology from all sciences and uses in an attempt to save humanity from using it against each other. However to do this, they have chosen that they need to commit genocide on all the species and Synths in the Wasteland to achieve their goal to save humanity: From Itself.
The Railroad believes Synths are slaves to The Institute. They have constantly tried to free them from the their clutches for many years, and have been partially successful in doing so. However, as shown in a specific quest, when let loose, they can be dangerous, and can bring harm to many innocent people. However the Railroad insists that the Synths still deserve freedom more than anything else. (Note though that they try to bring ones that they trust.)
The Institute makes the Synths. Their viewpoint that a Synth is merely a machine, and has no inherent consciousness like humans, and are more akin to a loaded gun, "... Whoever fired the gun is to blame, not the gun manufacturer.". Their goal is to advance technology underground and create machines as close to a humans image as possible for us to live on. But to do this, they reel in all the escaped Synths, and wipe their memory clean, raising another question if inhumanity can apply to a machine that can think.
So what do you all think? Who reigns as a superior ideology in the cruel world that is the Wasteland of Boston?