Very interesting article, Rob.
Fascinating to think of the game as a meta commentary on other games and game development. Not sure I agree, but fun to think about.
Initially, I wanted to poo-poo the connection to Bioshock. because I saw Zane's suit more like an astronaut (bursting with light), while the bigdaddy is a monster (darkness contained). I assumed they must have started AlanWake with the suit in mind, because it's so similar to an astronaut suit, then refused to change course later when Bioshock came out.
But while playing the game I noted other possible references. I wondered if one part with a large teetering crashed plane might be a nod to Lost (my initial thought was "man, you just can't do a crashed plane in the woods any more. not after Lost.").
And at another part, I was overwhelmed by the farm concert scenario, having just enjoyed the concert finale in L4D2. i remember strongly wondering who was ripping who off.!
Now, after reading your thoughts, I'm eager to go back and play much closer attention to the names and scenarios. Maybe they weren't coincidences?
Seems like someone could write a book on all the potential nods! heh. hmm.
(Like: are the clouds of ravens a nod to Gears of War? Was the initial car crash a nod to silent hill? etc.)