Speculative fiction refers to the genres of science fiction and fantasy.
If you are really going to play the genre card of how things are supposed to go or whatever, keep in mind that we are dealing with a game here, where people can select the fate of the narrative beats of the said game.
For example, if you broker peace with the Geth and the Quarians, you encourage a relationship between EDI and Joker, your character would be, logically speaking, more susceptible to Synthesis versus a character who is not. The evidence against Synthesis is there, but again, the major difference is the forced-choice dichotomy, free will vs. predestination of what Synthesis can represent changes that mindset if Shepard believes it. So how Shepard behaves is dependent on what narrative you have.
The internal logic of the character, and the person playing in that mindset, trumps the narrative every time. You are right, Shepard doesn't have hindsight or know everything, but Shepard also doesn't need it to make a decision that can be based on faith or feelings or logic, depending on how Shepard behaves.