Firefly Serenity: Simon and River Tam are not who you think they are

Despite what we are told in the Firefly Series and Follow-up film Serenity, Simon and River Tam are not Siblings. All their flashbacks are fake memories to strengthen the otherwise flimsy conditioning that they are siblings. Yes Simon Tam is a doctor. In all likelyhood he is the genius who 'cut into her brain' over and over. As of her Rescue, he is also her handler.
To off-quote some Blake's Seven: 'He stayed close and let her run.'
Of course he cant just lie to her because that would be transparent as hell, so his memories had to be adjusted as well. They had to share the same memories of childhood all the way up to his extraction of her from the Institute.

What does this mean? It means that River Tam's childhood memories can now be scrutinized. The young River Tam's game with young Simon about being an Alliance unit cut off and forced to resort to Cannibalism, and about being attacked by Dinosaurs suggests that the Alliance employed her tactical thinking to win the war against the Browncoats. It might not just be the current conflict, it might even be the next conflict that she is analyzing.

Of course, River is a Key, and that key needs to be pushed into a lock and turned so Simon is programmed with memories of his 'sister', and the reprogramming is proven to be working when the rebellious Simon Tam is detained in a Black-out Zone talking to disreputable people about rescuing his sister from the institute.

And so he Rescues his sister because he is also smart.

Of course the Operative sent to pursue River and Simon in the Film doesnt know about any of this. Because the right hand doesnt know what the left hand is doing. All the Operative knows is River Tam is a Psychic who was put in a room with the greatest minds of the Alliance and knows their secrets. What he doesnt know is that was the reason they all went to be in a room with River Tam. She is their Archive.

The motto of every government: Who Dares, Wins.