I like the theory, even if I don't think it's true. I feel like if Bethesda wanted to throw that curve ball at us, they would have made a terminal or something that would clue us in to his real identity. I mean without that definitive proof, we can't "know" and it is all just speculation. Honestly, based upon the thread title, I thought you were going to make the argument that Shaun is not Father because Father was fully formed by the Institute, and whoever Shaun could have been died when he was taken from the vault. That I DO believe, to an extent. I am not wholly convinced that an individuals nature doesn't play some crucial aspect in defining themselves (I would argue that it plays the greatest factor) but Shaun is certainly very... pragmatic, when it comes to assessing his own past. I know that the revelation that he leads the Institute is supposed to make you second guess everything you've heard about them and join their cause, but when talking about what happened to your wife and Kellogg, although it makes sense, it is incredibly cold and alien, even when he brings up that he has had years to make peace with it. The way he describes her death as her fault basically... I guess it would be the only way I could justify working with the organization that killed my mother in cold blood, but still.
I do agree though that the PC is for all intents and purposes a functional moron, which I H-A-T-E with a passion. Granted, the dialogue system isn't really supposed to convey intellectual aptitude and serves more to just advance plot points, but the contrivances of the story (and overall game content) seem like blatant slaps to the face over the hours spent playing. I think the idea was to make him as relatable as possible, so that way his mannerisms would fit a broad range of people's preconceptions for "who" their sole survivor is, but it comes off as appealing too much to a common denominator. Which isn't to take anything away from the voice acting. I think the voice acting is great. And honestly, a lot of the problem comes from the tonal whiplash, like when you go from looking for Shaun, which is a tense and frantic thing, to doing [censored] favors for some random dude you just bumped into. The duality of video games trying to tell a story essentially, eh?
What they should have done from the start, since all dialogue options serve to advance the story in identical ways, is make four different personality types, such as: straight-laced and polite, foul mouthed and lovable rogue, sarcastic and joking, and then suspicious and mean. Or honestly, however you'd want to divvy that up. That way, we can at least dictate how we are going to act for when we meet certain people. For instance, if you are talking with someone you think is cool and you are trying to break the ice you can be straight laced, but if you run into a tense situation you can be the foul mouthed rogue, or just mean and direct. I think the dialogue was written so it tried to accomplish that, but it was hit and miss in my opinion and I would prefer to have more direct control when dictating how I want to respond to any given situation.
edit: Sorry to go so far off topic there at the end. I forgot to mention that I don't think it's true that Shaun isn't Father, because to get a DNA sample, they wouldn't have to puree baby Shaun into some organic goop. You could isolate DNA from any culture of cells and then amplify from there. Killing the infant Shaun would be evil for no discernible gain, which doesn't sound like the Institute's MO (and honestly sounds like some 1970's villain caricature). Twisting the kidnapped young boy into the essentially psychopathic leader of your organization? That fits them quite nicely.