Ratner never filmed the scene of Mystique playing chess with Magneto. She was originally going to be in the scene, but Rebecca wasn't available, hence, it's just Magneto. Would have been a pretty dumb ending to go that route, I agree.
1) Young Angel cutting his wing and in his very next scene accepting his mutancy without any reasons given?
-I agree, Angel's arc in the movie was handled very poorly. I believe he had an amazing set up (opening flashback, and sequence at Worthington Labs), but it had absolutley no payoff, or any semblance of explanation behind his motives. This is one area where I will concede bad writing.
(2) Storm strongly & violently opposed to anyone taking the cure but in a couple scene later seen defending the cure and not blinking an eye when Beast and Wolverine used the cure agt Magneto without any reasons given?
-I think it's more of a "are you ready to do what you need to do when the time comes" moment. For the good of the whole, Magneto had to be stopped by any means neccesary, and that meant curing him. I don't have a problem with this.
I would have liked, however, some more time devoted to explaining Storm's stance on the cure, as well as other mutants. It was "We're not a disease", and then nothing more was given to that thought.
(3) Beast supposedly rejecting the cure because it had been weaponized but in a couple scene later used the cure as a weapon agt Magneto without blinking an eye?
-See same response to #2.
(4) Storm reading the eulogy abt preserving Xavier's vision and in the very next scene discussed abt closing the school?
-I again feel this was a bad scene. This scene, as well as Wolverine packing up to go off and find Jean, and his interaction with Storm, were the 2 worst scenes of the film. I think these scenes epitomize the bad writing of this film, and it is in these scenes that the movie manages to get everything wrong. Beast wants to close the school, but is happy when Storm steps up to take over.

Beast wants to honor the memory of his mentor, and father to many, Charles Xavier, by closing down his school in the first place.

I concede this scene to you as "bad writing".
(5) Multiple Man out of prison in one scene and back right in willingly in his very next scene ?
-I think Multiple Man's recruitment into the Brotherhood in general was pretty poor.
"I could use a man of your talents." "I'm in."
WTF?!
That was just pretty bad.
(6) (deleted scene) Mystique abandoned subsequently betraying Magneto's hideout but in the final scene seen playing chess with Magneto without any explanation?
-That scene was never filmed, but I agree, it was a bad idea.
X3 is loaded with such contradictions and that I believe the fault lies squarely with the director rather than the writers. I cannot believe any hollywood screenwriters can make such mistakes in characterisation apart Ratner's directorial style & his very short attention span!
I agree that there were many mistakes in this film. I don't believe it's as contradictory as you claim it to be. I feel that the movie worked more than it didn't. That doesn't mean there aren't parts where it didn't work for me, however.
Your point about Xavier being Jean's "Stryker" and the mansion being her "Alkali Lake" and why she didn't flip out; Xavier explicitly states in a scene prior that it is "unclear how much Jean knew", which explains that she didn't know what was going on.
Jean knew that Xavier was helping her to develop her powers, as stated in
X-Men... but during those sessions is when he could have put in the blocks, and she'd never know. It's explained that she doesn't know what's going on, so it'd be hard for her to "flip out"