I think the big problem with "Alan Wake" was simply that they changed the plan in what seemed to be the 11th hour. I don't think people were intrigued originally by the whole "Flashlight combat" aspect of the game or the "light against darkness" theme, but the idea of a sandbox survival horror game... which is not what they wound up producing. I think when it became known that the game was not going to be a sandbox title a lot of the interest went elsewhere.
Also I think a lot of the problem has to do with a very limited bestiary (I mean you can only kill the same axe wielding shadow-logger so many times before it gets old, they needed a few more models at least), when your dealing with a game this linear it becomes really noticible.
I also think that "Deadly Premonition" had something to do with it's poor sales as well. While I haven't played it much yet (though I have goofed off with it), DP *IS* a sandbox survival horror game, and arguably the style of game that "Alan Wake" was supposed to be. DP suffering from very dated (PS-2 era) graphics, and a lot of bugs, but it was also a FAR more ambitious project and sold for only $20. It's been called the ultimate cult-sleeper hit of this console generation by a number of people. Honestly, I think "Alan Wake" got upstaged by a game that was one third the price and technologically inferior, largely because it was serious about at least trying to do what Remedy decided they couldn't pull off.
Also I think one of the other problems with "Alan Wake" is that it's ridiculously derivitive despite the story being told well. Most other horror games have some wierd twists you don't nessicarly see coming. Even at it's worst "Silent Hill" almost always has a cool angle, and "Deadly Premonition" had some interesting bits involving the voice in the protaganist's head (and let's be honest, our hero in DP was a lot more creative than Alan was).
"Alan Wake" pretty much took half a dozen fairly popular horror stories ("In The Mouth Of Madness", "Twin Peaks", and unapologetic theft from Steven King where they even admit this themselves during the game as sort of a joke) tossed them into a blender, and then fired it out of a shotgun. The pretentious quoting of Steven King in the first 15 seconds of the game about how "horror is scariest when it doesn't make sense" came accross ultimatly as being a cop out for the fact that they weren't even going to bother to try and explain themselves and just shoot out wierdness for the sake of wierdness, and not worry about reconciling things at any point. Being unable to come up with a consistant plot and satisfying conclusion does not cease to be a problem just because you admit it and quote a well known author (who himself is increasingly criticized for exactly the same thing... ).
Don't get me wrong, the game is a noble concept, and honestly it has some moments of pure genius (I especially like the 'Night Springs' segements) but in the end it wasn't anywhere near what it could have been, and arguably should have been given the lofty promises and enough development time where we should have seen those promises delivered on.
I've played it a bit, and while it is a good game (do not misunderstand that), it's not an "OMG, this is so amazingly awesome it defies belief" game... and really that is what Remedy set their sights on producing and the expectation by which they are defining their success.