I disagree. On the first point, after I heard the commentaries, it became clear what they were alluding to in the game. It also put a lot of things together, but these were all things that were hinted at in the game. Yes hinted, there was no guy in the game saying "Oh, OK, let me put everything together for you so you can have it all neatly wrapped-up like any old Hollywood movie"... Seems to me like today, both in games and movies, people have to be hit over the head in order to understand what's going on. If a movie/game leaves things open for interpretation, or you have to try and put things together yourself, you get similar comments to what you said above. I'm sorry, but I don't agree with that attitude. I think allusion, symbolism, all these things which are common place in books, should also be there in games and movies. They were certainly there in Heavy Rain, and it was easy to miss them. Nevertheless, it all came together very nicely in the end.
OK, as for the murder in the clock store. How exactly is that a plot hole? In fact, that is a huge clue as to whom the murderer truly is. In fact, it really shows you whom the murder is before the revelation. At that point, after the clock scene, you should be saying "what the... this isn't right! There's no way that could have happened as he [you know to whom I'm referring] said. Therefore... could it be?" Remember, you don't actually see the murder take place. Sorry, I see no hole here.
edit: if you think there are other plot holes, I would like to hear them. Also, if you still think the clock scene is a plot hole, I would like to know why?
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.