If the player decides to go along with the Institute, is there any logical explanation as for why they don't/can't recreate their husband/wife as a last generation synth?
And to that effect, why do you suppose Shaun didn't recreate his mother/father previous to the protagonist meeting him as another bargaining chip?
It seems like it would be a fairly rational thing to do for someone who has that power.

I'm just speculating here, but I don't think the Institute ever had the power to snap their fingers and perfectly recreate the likeness and personality of another human from nothing. They always had to have that person in their possession before they could have the information they needed to make a copy. In the same way I can't make a VHS recording from thin air, it has to come on TV before I can make a copy.

Nora/Nate had long since been dead by the time the Institute had the technology they needed to make Gen 3 Synths so it was impossible for them to go collect that data and Shaun wasn't even old enough to remember either of his parents.

I was more thinking in response to Shaun knowing that his surviving parents was searching for him. It would have been perfectly possible to recreate a Nora/Nate synth based on the corpse still in vault 111 and implant it with fake memories. Promising the player the return of their spouse seems like it would have been a much more convincing argument than getting a fake kid based on your elderly son.

@"Waffenbaum" Maybe there's something explaining why in the terminals, because the only possible explanation that I can think of as to why they didn't, is maybe they can't replicate someone using dead cells.

it was cut content  but the files have been found and recreated in a mod called Synthetic Love on the nexus. It adds Nora as a synth in Diamond City and it actually uses Beth's unused dialogue from the cut content by my knowledge. Lines for affinity, companion perks and everything is included.

Also I think it's because she'd been dead for decades once Shaun became Director and there just was no way to bring her back. This was probably Beth's mindset too and why they cut it out.