It would have been more interesting if Shaun and the wife had both been taken and you eventually find out that shaun runs things but that it was your wife that was behind the massive growth of the Institute and maybe she created their bladerunner branch or even if she created the railroad to battle the institute after losing the kid to them. It would have led to things being more complicated and interesting then just a kid nobody cared for in the game as in a way it'd be that choice nobody wants to make of "do i save my wife or save the child and lose her" that you see now and then in the news.
Biggest issue with that is that then the romancing companions would be really out of place. Not to mention the fact that you weren't thawed right away would be a much bigger issue of blame.
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