How did Xavier know Jean was her parents home if cerebro was destroyed?
Xavier is a telepath, and he must have a stronger psychic connection to those he knows well. He sensed Jean had left the mansion. We dont know if he read her mind to know her destination (if she was on her way there) or her location (if she was already there). Its a wonder you dont harp on about how she got there. Jean going to her parents is obviously to show her seeking a place of familiarity, as she believes the mansion can no longer be her home because of Xaviers meddling and the death of Scott. Shes leaving that part of herself behind, knowing she does not want to be caged or fixed. In the comicbook Phoenix Saga, Dark Phoenix flew into space and when she returned she did go to her parents home, seeking some sort of anchor through familiarity and family love.
Did the brotherhood and X-Men arrive at Jean Grey's parents house at the same time?
It looked to me like the Brotherhood were lying in wait for the X-Men.
If the brotherhood arrived at Jean's house before the X-Men why didn't they try to take Jean then?
I believe Magneto knew that Xavier would come (alone or with others) and he knew his only chance of getting Jean on his side was to discredit Xavier in front of Jean, to make his own cause look more appealing. By reinforcing Jeans fears of being held back, caged or cured, Magnetos fight for freedom looked a better option.
Why were Logan and Wolverine the only X-Men that went along with Xavier to find Jean?
You mean Storm and Wolverine. Well, they are the only adult, non-student X-Men at the mansion. Colossus, Kitty and Iceman are younger students who hadnt graduated as X-Men until before the final battle. The early part of the movie shows Wolverine telling Storm the others arent ready (for conflict situations).
Did Xavier not consider the possibility that they could be outnumbered if Magneto and his brotherhood tried to take Jean?
I dont think Xavier would have been aware of Magnetos expanded Brotherhood at that time. As far as the X-Men knew, Magneto had two associates (Mystique and Pyro) and Mystique was incarcerated. The X-Men would not necessarily have known that Magneto was building an army and gathering others to his cause.
Why does Juggernaut throw Wolverine into Jean's house twice after Magneto tells him to keep the X-Men outside?
Storm also does something similar, in blasting Callisto through the door. I dont think a mutant battle could tip-toe gingerly around the house and avoid damage to it or incursion into it. Thats not the nature of superpowered mutant battles. As soon as Wolverine heard noises and decided they had to go in, the Brotherhood just had to stop them getting to Magneto, Xavier and Jean, which they did. Juggernaut is obviously just a musclehead and is dozy enough to throw Wolverine into the house
but of course Wolverine had to get inside in order to be a witness to Xaviers demise, so story-wise, it served a purpose. One way or another, Wolverine and/or Storm would have got inside.
Why doesn't Arclight use her power in this scene?
Her power creates sonic shockwaves that can shatter inorganic materials by finding the frequency at which they break. Storm is very organic, as is Wolverine (and his inorganic adamantium would not be shattered if she targeted that)
Why was Magneto's right hand man(Pyro) absent from this scene?
He was away on some sort of mission that ends with him fire-blasting a clinic.
Why did the scene of Juggernaut grabbing Wolverine, throwing him threw the ceiling, and Wolverine failing threw the floor defy physics?
I dont see how it defies physics. Wolverine has a super-dense skeleton, coated with the densest material known, so hed fall pretty hard and fast.
How did porcupine boy expect to fight Storm considering he has to give all his victims a bear hug to kill them?
I dont think Quill expected to fight Storm at all. Like Arclight, he adopted a defensive posture, and he probably had basic fighting skills, but he stood little chance against Ororos tornadic twirling. Which was the point. To show Storm kicking the crap out of them and then zapping Callisto. Thered be little point in showing her rising in the air, creating a vortex and spinning with it only to be hugged to death with a spiny embrace.