Throughout the game there are hints and outright statements/examples that someone can be a synth and not even realize it, with a full set of back-dated memories. The whole Blade Runner problem with Rachel and Deckard (yes, he's clearly an android), which was repeated in the reboot of Battlestar Galactica.
In Fallout 4, Danse is one example of an unwitting synth, the mayor of Diamond City is another, those farmers, etc. Hell, when shooting up the Institute I noticed an awful lot of the scientists were also synths (black blood)(yes, I mowed down a room of unarmed scientists because screw those guys), and earlier tours of the place didn't give any hint that they knew they were synths. There WERE humanoid synths in the Institute who DID know they were synths, but none of the scientists ever behaved that way.
So why do we assume that the Sole Survivor himself/herself isn't an unaware synth? All of his/her memories pre-war could have been fabricated. The thawing-out sequence could have been staged, and the Sole Survivor set loose to (hopefully) wreak havoc on the Institute's enemies. Really, the only evidence I see that Sole Survivor is NOT a synth is the fact that going that route doesn't present any obvious upsides for the institute. What was the Sole Survivor intended to do? What was the mission the Institute wanted completed?
The thing is, that same problem applies to the decision to leave the Sole Survivor alive and then thaw him out if he IS real. All of the same risks of unpredictability were there, as was the lack of a clear upside for the Institute. When I did my playthrough I kept expecting Shaun to reveal that he was running an elaborate long con and that he'd thawed his dad out so that revenge would be taken against the SOBs that killed Shaun's mom and kidnapped him. That would've made the rationale for thawing pops out more clear, but they (Bethesda) didn't go that route. Then again, if Shaun just wanted revenge on the Institute he could've played along until he got the necessary access codes and then set the reactor to go critical. No need for dad to get involved.
Seems to me like playing around with the Sole Survivor's true nature could make for a really cool DLC.
Thoughts?