Because that guy is the end-all be-all judge of story content. There are some silly things in there (like EDI's sensors being able to tell the things a Reaper), but they used Saren (an organic) in ME1. They'll use organics, especially when they're under their control like the Collectors. As for the final choice, its not really as binary as it seems. Its actually incredibly tough to abandon the "good shepherd" morals to have an advantage against the Reapers, or abandon that advantage, and yet still have a conflicted conscience.
There are a few more points that are just plain wrong. Like the game over screen bit. Cerberus doesn't make money from colonists disappearing, and the Lazarus project took a damn long time to get going. The point about Geth Slaves? The whole deal with Legion is reprogramming the Geth that worship the Reapers! The point about the alliance and the colonies? There were thousands of people missing, and at the other colonies, they got there too late. At Ashley/Kaiden's colony, you got there while they were still in the process of collecting humans. He's just reaching to find more things wrong with the game than there actually are.
He does have a point about how Mordin got that Collector bug though.