On the 1st point, could you give me a summary of what the commentaries say?
I don't actually own the game (borrowed it from a friend), so I don't have the means of checking it myself. Could you tell me what exactly the reasoning is behind this?

As for the clock store, I didn't call it a plot hole as much as I called it a cheap and deceptive plot device, and I stand by that.

It's been over a year since I played it, so I don't remember all that was said in the commentaries (there are 3 I think, or at least three), but you should be able to find them online. Let me know if you can't find them. As for the clock scene, I really don't call it cheap. Remember, the killer was very manipulative, on more than one occasion. Just because you did not figure it out back then does not make it cheap in my opinion, rather clever Also, it's not as if the game pulled a fast one over your eyes, you were being manipulated, but you had all the clues. So far, despite some people's comments that there are "plot holes", I have yet to have any concrete examples of such.

BEGIN SPOILERS (highlight to show):

First, the murder at the clock shop is exceedingly cheap because you the player are controlling the murderer and you do not murder anyone.  There is no break in the action and you never lose control of Shelby.  You the player walk in to find a man dead that the game later tells you that you killed even though you know that you did not since you were Shelby the whole time.  This makes absolutely no sense.  It's not a plot hole, it's just nonsense, and it is in no way clever.  Imagine if at the end of a Mario game, they went back and showed you a level you already played but then edited in you killing Luigi to explain why he wasn't playable in the game.

The plot holes for me all have to do with Ethan.  The game makes no attempt to explain how Ethan ends up far away from his house with Origami figures in his hand after he blacks out several times.  The blackouts themselves are explained by the shrink as being a side effect of Ethan's concussion, but the game never makes any attempt to explain the rest of it.  It seems to be in there solely to make Ethan a probable suspect in the player's eyes.  I agree that storytellers shouldn't beat their audience over their head to make a point, but this is pretty big plot hole that is not explained, and a viewer should not have to watch a commentary to get insight into it.

There are other plot holes involving both Madison and Jayden who both possess a supreme ability to figure things out off screen all on their own, but I am willing to concede that due to their occupations, it is reasonable that they could figure these things out.

END SPOILERS

I'm not sure why you're fighting so hard to defend this game.  I liked it too, and I'd recommend it to others, but it's flawed.

Got an error message that resulted in an accidental double post.

Not really fighting, as trying to figure out if there are any plot holes. From what you said, the only possible plot hole is during the clock scene, but if I recall, what you said is not correct, and it does not amount to a plot hole. However, I would have to replay that to be certain. Other than that possibility, there are no plot holes that I know of. I think someone should be able to explain why he/she thinks a game is flawed. To be honest, my experience is when you ask people to explain their reasoning (not just in games, but in many things) the real answer is "I just didn't like it" or "That's just how I feel". I can respect different opinons, but that's VERY different than being "flawed". No hard feelings I trust. I really hope they release a spiritual sequel.

I think both Xlord and I did a perfectly good job of explaining why we think the game is flawed, but you just keep hammering on about plot holes.

Fair enough, we're just not going to see eye-to-eye. I personally think the only minor flaws are graphical (a bit dull in a few places), and the play control is a bit stiff at times. Nevertheless one of the best games I've played. Of course, to each their own

edit: and I was hammering on the plot holes because you said the story "was a complete mess", so I figured you meant plot holes, but now I'm guessing you did not (although Xlord did mention plot holes). Anyway, let's give it a rest. Let's move on to another game...

Did you read what I said? I outlined a very specific plot hole in the second paragraph of the white text which you have not addressed at all.  Do you think it's perfectly acceptable for this part of the plot to be left unexplained?

My apologies! You're absolutely correct, I forgot to address that issue. So here it is (highlight to see):

Remember that Scott (the killer) did see Ethan's son die in the accident. At this point, Scott saw a new target (remember he had been "searching" for a "real" father for years (ie killing kids for years). He even mentions that he was inspired by seeing Ethan trying to save his son. Scott studied Ethan. This is undeniable, given all the clues that were left for him and the scenarios he (Ethan) had to go through. Now, you do have to make a speculation here, but it is entirely reasonable and plausible. That is, Scott found out about Ethan's blackouts.

Now these blackouts provided Scott with a scapegoat! Remember, Scott is clever, knows how the police operate, but is not invincible. He knows he will likely be caught... unless someone else takes the fall. In which case, he could continue with his operations (if he so chooses) or just stop (he might have decided that no one, is worthy of being a father). Anyway, Scott could easily manipulate Ethan. He passes out, so Scott could easily put him in his car, drive him where he wants, and place an origami figure in his hands. Scott set up Ethan so that Ethan began to believe that he subconciously might be the killer. At the same time, this allowed Scott to go back and take any evidence that might incriminate him (such as the origami figure he gave to Lauren. Where did Scott drop off Ethan? Carnaby row, which is of great sentimental importance to Scott. Scott lived there, AND that is where his brother died!

Hopefully that explains the issues with the blackouts.

That's a good enough explanation in the context of the game, and had the game included that, that would have satisfied my curiosity and not made me feel like something was missing.  Would it have killed them to add another 30 seconds to the ending showing a few quick cuts of what you described?

Anyway, I noticed that no one's discussed The Taxidermist DLC in this thread yet.  For being as short and oft criticized as it is, I really liked it.  The sense of dread is well defined and the short run time makes repeated playthroughs to get the five endings a snap.

HIDDEN SPOILERS:

I remember being angered by the thought mechanism of the game. It's awfully convenient how you NEVER get to read the true thoughts of the killer. I can buy that his personality would completely change after the reveal (because he's clearly a good actor) but it's impossible to keep inner thoughts secret.

I can see why not including that explanation in the game is annoying. At the same time, I'm a bit glad they did not include it. I think it's nice to actually have to figure things out. Again, it can be annoying, but as someone who enjoys a good mystery, I actually enjoyed pondering why those things happened 

I don't have internet at home, so I never got a chance to play the Taxidermist episode. I was hoping they would release it on disk eventually, but alas no avail...