More spoilers ahead (though the spoiler-shy should have deserted this thread by now...).
My problem with Alan is, that I consider him a sociopath. It's probably not in the story writers intention, but there are many things in the story, that give me this impression. and I know that I won't find many friends for writing this.
As we know, whatever is written in the manuscripts does happen and Alan wrote it.
In addition to Stevedog13's points, I'd add the following:
* In one of the cabin videos (in Rosie's trailer) Alan mentions that his script is being aggressively edited by Jagger. This supports the argument that he has to include bad events and the death of bystanders (the most morally objectionable of which occur off-game like the Taking of hunters, woodsmen and campers simply because they were in the area).
* Dr Hartman was involved with events well before Alan appeared on the scene as Thomas Zane's assistant, and may well have been responsible for his downfall.
* At the end, Alan effectively sacrifices himself to save Alice.
There's a lot to dislike about Alan's personality, but I would say that it adds depth to the story to have a flawed protagonist. If anything, it might have been better to include it as a game mechanic (be an utter b*st*rd and gain a greater ability to manipulate the plot to make things easier, or be nice and have the Dark Presence take greater control and impose tougher challenges).