First let me start by saying I loved the documentary, and found it both distburing and beautiful at the same time. There were some questions I was left with at the end but overall, I recommend it.
I was quite surprised though when I saw people in the reviews on here questioning if this could all even be real, or whether it was some sort of story the brothers put together. I've seen some mention of whether someone could wake up and only recognize one thing (in this case, his twin brother) but the fact remains that we actually know very little about the brain. We don't even know how many neurons are in the brain, and you'd think that would be a good starting point of something we'd know by now, but it's still uncertain. Strange things happen within the brain and just recently a woman in the UAE woke from a vegetative state after 28 years, she is now speaking in conversations and undergoing physical therapy. The fact remains that the brain is a mystery and how it exactly works is based a lot on theory, in fact there's an entire field called brain theory.
The second thing I saw criticized was the question of how a 14 year old boy could take a subway home and no one think anything was out of place (in 1978). And those who make this comment obviously have no understanding of British culture. As someone who lives in England I'm here to tell you if "minding your business" was an Olympic sport, the UK would win every year. People don't even like to look at each other on the subway here. So for a teenager to take the subway at home by himself in the late 70's and no one be concerned or question anything is totally believable to me, someone who currently lives in London.
I feel the people who are nit-picking are doing so because the story is just so remarkable perhaps. But the fact remains we know very little of the brain and how it heals itself after trauma. And that is a scary fact.