Spoiler Alert : If you have not completed the game please do not continue reading. 

I will bring up some plot points that raise questions and then I will provide some insight on possible answers to these questions. 

At the beginning of the game ( in the dream) You are greeted by a mysterious light. The light aids you in your dream but it is not revealed who or what the light is. The light mentions " For he did not know, that beyond the lake he called home, lies a deeper, darker ocean green, where waves are both wilder and more serene. To it's ports I've been. To it's ports I've been."

Later in the game you gain bits and pieces of a famous poet Thomas Zane. You find out that his wife also drowned in the lake in the 70's, his wife is Jagger aKa the woman who symbolizes the darkness. You also find out he wrote himself out of existence except what he left inside a shoe box.  You write him into your story as the light to save you from the cabin where you are being held, you free him from the grasp of the darkness and he saves you and scatters the manuscript. This means that you wrote him back into existence. You also find out however that he wrote a short biography about Alan wake when he was 7 and wrote about The Clicker. This means Zane wrote the clicker into existence and set the whole line of events into motion. 

I would also like to bring up when Thomas Zane is talking to you and you see a copy of you " Mr. Scratch" it is not explained who this is or how they tie into the story. Zane says to you that he will be taking your place, and by this I presumed that Zane knew that you would have to sacrifice yourself for your wife. You don't know however what happens to Mr. Scratch" 

I made a connection with the first actual line of the game and the last line as well. At the start of the game the first words you hear are Alan, Alan Wake up. the last line of the game is also Alan, Alan Wake up, except with a darker tone. The beginning wakes you up from the nightmare you have. The ending phrase is said after you are taken by the darkness and your wife is saved. Could this be a cycle of some kind? 

I want to go back to my first point and elaborate at the end of the game the last words Alan says are " It's not a lake, it's an ocean." This is completely out of the blue and has nothing to back it up. However on my second  play through I picked up on this at the very beginning, That Zane try's  to tell you something but at the time you do not understand. I want to take apart what he says "Beyond the lake he called home, lies a deeper darker ocean green." This directly ties into Zane's story. He is the one who named the island Diver's isle, he is also the one who was trapped beneath the lake.  This means that below the lake it goes far deeper and that it could be the source of the power that allows both of your writing to come true. He also emphasizes "To it's port's I've been" Meaning he has been there before, but I believe this has more behind it than we know of at this time. 

After part 5 you go into a cut scene and Zane is talking to you and you are looking at a copy of yourself. He says he will be taking your place. Zane knew the consequences that Alan was going to have to accept when he went to fight Jagger. Zane had lived through this before and he knew that Alan would not be able to save his wife without sacrificing his own. So I believe since Zane had written the Clicker into the shoe box and had actually written part of your life he put his plan into action and it all eld up to you having to defeating the darkness using the Clicker. My point is that I strongly believe that You are not playing as Alan in the end but you are Mr. Scratch, and that Alan is still alive, My only support for this is the final line of the game, Alan, Alan Wake up,( this means that you are alive and not actually trapped in the lake) which is how the game began and I believe it is how the game will continue. The only explanation I can give is the game features a sense of lost time. It is likely that there is another time gap and you wake up again and do not remember how you are there but that you are still alive, but you may not know Alice is alive. So I believe you are still alive and ar enot trapped under the lake, but that Zane saved you from the nightmare he has to live in. I figured it was a pretty solid explanation and i'd send this to you. Please tell me what you think of my Explanation and add if you have any extra info.