I think that this is the right place, so we'll begin after the final warning:

Spoilers are held within.

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Firstly, my understanding of what happened when they decided to throw my previous understanding of the story out of the window and into a sudden mushroom cloud is that they were actually being quite clever - forcing the player to make up his/her own mind and grapple with what could be seen as a few very, very cold choices. It's almost the spiritual promotion to some of the contracts in Oblivion's Dark Brotherhood questline.

But my interpretation is thus: Father is likely the real Shaun, and the boy at the end is likely a synth/cyborg/possibly the real-hypnotised-Shaun if he is indeed the boy/synth/PRHS encountered at the same time as Father earlier on.

But there isn't actually any proof either way, is there? It seems to me that however unlikely, Shaun as he claims to be at the end is actually possibly the player's son.

And as a side note, I agree completely with the ending monologue - the Great War ripped most of the player's world apart, and I would add that the Institute stole his/her remaining family. The companion and romance options are thus utterly necessary and ought to be lauded, in my opinion - should one desire a new family, that's how one will likely obtain one after the timeline ends.

Thoughts?