Okay, we know that from X-MEN: DAYS OF FUTURE PAST that this movie is longer a part of the film canon, but let's take a look at what could/should have been done to save this movie (it's easier than you might think.)
We all know that X3 had zero character development, a plot that came WAY too early in a franchise, and … THEY KILLED PROFESSOR X … simply because the writers couldn't think of a way to neutralize him in the movie in order to make Jean a bigger threat to the X-team (and then after the credits, he's back in some brain dead guys body … but with the same voice … despite now owning different vocal chords. Some have argued that it is the body of his identical twin, in a coma since birth … I don't buy it, but I can accept it.)
So, in the opening scene of LAST STAND (cringe title) we know that Charles created mental barriers and other obstacles inside the mind of Jean Grey to keep The Phoenix locked away and was able to do so at all times, from afar, seemingly without much effort … so in order to neutralize Xavier, all you have to do is have Phoenix tell him something along the lines of “You locked me in a mind for 20-years, unable to move speak or scream, now feel the same as I lock you inside your mind for the rest of your life.” … have her touch or kiss his forehead for a visual and BOOM! Professor X is in a coma-like state, and the only way to break him out of this 'spell' … is to kill the Phoenix (breaking physic control over him so he can and wake up.)
And if you don't want to kill her to break him out of it … have the kid whose ability stops the abilities of other mutants from working get close to Phoenix to shut her down temporarily and free Charles from his coma and re-lock Phoenix away again for possible use again down the road and putting Jean Grey back into the franchise without cheapening it.
And as for Scott Summers, you don't kill him either, what you do is …
While Phoenix doesn't NEED his protection, you COULD have him stand by her side all the way. Have her flood his mind with all the good feelings and memories he has of and for her in order to keep him under her complete control without having him simply be her own little zombie. And when Wolverine tries to get close enough to kill Phoenix … CYCLOPS VS WOLVERINE!
Something everyone wants to see, not that Iceman Vs Pyro crap … but Wolverine knows he can't kill Scott, he's under a kind of spell, it's not his fault … and he knows he'd kill for Jean too, so it wouldn't be right.
The opening scene with the big robot … B.S!
The Sentinels are a BIG deal in the comic-books and are a part of a HUGE story. So are we to REALLY believe that such inventions were around pre-X1 without them ever being mentioned?
No. That little nod to the audience was the waste of a future movie (or FUTURE PAST movie ;-) )
Also, the training room is supposed to be a realistic training simulation to prepare the kids for future missions. They need to figure things are themselves. Don't have them fight alongside Wolverine, who can take out practically anything on his own. Are you serious? Get rid of this sequence and replace it with another scene. Maybe the wrap-up of another mission or something.
Are we to believe that Wolverine was actually there because someone thought he needed the practice? I doubt it. Even Storm told Wolverine he should let the kids do more for themselves, so why is he there in the first place?
In the final act, Magneto goes after the kid, and it's X-Men Vs Magneto's Mutant Army. Magneto lets the pawns go first … but at no point does it occur to him to manipulate the metal in Wolverine and control his body to make him fight for him against his own team.
Now THAT would have been epic (and would make for one hell of an interaction between the two characters when Erik is powerless at the end.)
Anyway, that is how I would have changed the X-Men 3 script for the better so it wouldn't suck like it did (remember, MATTHEW VAUGHN was weeks away from directing this, so it's as much his mess up as Brett Ratners as M.V approved the script. Love Vaughn, not trying to stir up hate, just saying.)
So, before I go, let me just note an issue with X-MEN: FIRST CLASS.
We know from the first film that Eric helped Charles build Cerebro … yet in first class the Government have the original device … despite not yet knowing that such mutants exist. WTF? They SHOULD have had a Government person ask Charles “What do you need?” to which he replies, “Actually, there's something I've had in mind for a while, but I'll need a big budget” then cut to Erik and Charles going over plans for what Charles has had in mind for a long time.