I'll try to answer some, although having not seen the show these responses are only assumptions.
generally when people point out plot holes (like the thread about wicked) I just assume there is a reason for it and it does not need explaining)
Who is Mr Y's interior decorator? His room seems to change as the plot dictates- first just the strange cubicle for robot Christine and a piano, (nobody lives in that room!); then it has its entrance in the middle of the floor- that seems to have been added later (lord knows how people got into the room before that). Then, just so that Mr Y can sing about creepy stuff the chandelier and strange statue appear. Is he still moving in to this new pad or has he just been to the Coney Island boot fair?
I think on the CD I got the impression that the 2 scenes happened in different locations within the aerie, perhaps different rooms "Is this where Mr Y Lives? This is where he works" having not seen the show though, I dont know if the sets are similar, like if the big gold woman is in both scenes.
Then, considering there is only the one entrance to the aerie how does Mr Y not notice Madame Giry and Meg hiding in the corner?
Maybe they were there before anyone else got there, like spying on the Phantom's new work?
Why has Raoul become so utterly opposite to his earlier portrayal? What is the motivation?
I think it is just to create a "villain" but we see all the time on TV that people are one way when they are courting and another after marriage
Who keeps a gun lying around on their piano?
Why try to kill yourself when you are hatching a plan to bring your true love to America?
See thats my gripe aswell, I;ve said before that this scene should be " a few days before the arival" not 3 months before, that way the phantom would still sing till I hear you sing again, but all the stuff afterwards would be about his plan coming together and tomorow she will be here, not "how on earth will i get to hear her" when it is obvious he has a plan already.
Why does Gustave not wonder why a man in a mask is talking to his mother? He certainly doesn't ask about it (perhaps that would be rude?) Is it really enough to make him forget his terrible drowning nightmare?
I think he already realises who it is, the owner of the place, if not he is quickly introduced and is already fascinated by the place, as a child if you were to excited about meeting the owner, and finally do, then you tend to forget about recent things like a bad dream.
And doesn't anyone wonder why Mr Y exits via the balcony?
Why does anyone do anything? ifs more interesting that way.
Why couldn't the resourceful Mr Y escape Paris with money? He obviously hung around long enough for the oh-so-believable night with Christine (when he was 'no longer shy'- ah, so that's it, he was just shy in Phantom 1.)
Bad Exchange rate at the time? I never got the impression he was loaded to begin with.
How does Mr Y know meg will be on the pier with Gustave?
Well meg made no secret that she likes to go there all the time, and I'm sure the Phantom being who he is, he knows his employees well.
Oh and why does Christine employ such a crap nanny? That kid wanders around on his own all the time!
There was a nanny?
Oh and what the hell is he doing singing (endlessly) up a ladder?
Huh?
Why does Madame Giry just run off after the gunshot- she never returns with help?
It isn't necessary by the time she gets back she would be dead anyways, I don't think there was 911 back then
And here's a big one- would a dying mother really ignore her terrified 10 year old son as he crouches in the corner, in favour of singing to- well, just about anyone else? Boy, that kid has messed up parents!
Thats the big problem with the ending. you need to accomplish too many things that just can't realistically happen so soon together: She dies, she tells the boy who his real father is, she says goodbye to the boy, but also has to have a moment with the phantom, the boy accepts the phantom as daddy.
Why is the stage so empty most of the time?
Maybe it is a conscious decision, maybe there is no more room for sets? what is disappointing about this is it seems to me that the show is designed only for orchestra seating.
The ending scene, isn't it supposed to be the same pier that "floats" above the bar? is it an actual pier set above the bar? couldn't they have the action on the pier suspended half way up in the air with a projection of the waves below or something?
What has the show logo (and house cloth) remotely got to do with the story?
Was told it is robo-christine's face plate after the "fire" that does not happen
Now im not saying that my answers in any way should change opinion of the show, I'm just pointing out how things could be spelled out better and you really should not put out things in a show that are not explained enough or talked about enough that the audience needs to guess about their meaning or answers
http://www.flickr.com/photos/27199361@N08/ Phantom at the Royal Empire Theatre