I think he's guilty as fuck. The one bit they left out about Brendan's mom seeing a lot of blood on his pants the same day she went missing is compelling, and it really bothers me that it and other evidence was left out.
That said, I have no doubt there was a lot of shenanigans going on with the investigation and prosecution. The way Brendan was treated/handled was a travesty of justice, and he most certainly deserves a retrial. 70 IQ, easily and he's easily manipulated, "[he just does what he is told]" by all accounts.