It does not "blatantly contradict" X3. Stop saying that, because you know it's not true. If it's being friends with Magneto in the 80s, keep in mind that Magneto still hasn't helped Charles rebuild Cerebro so clearly their relationship goes back and forth over the ensuing decades. If it's Xavier walking, he can project an image of himself walking into people's minds, or he could have been experimenting with a cure for his paralysis. You can't prove that neither happened which means you can't prove that X3 has been retconned, or even have strong evidence. The characterizations of Mystique and Beast tie in directly with First Class so you can't really use that as ammunition to shoot down X3, either.
Wolverine looks more and more like it is probably getting the boot from continuity, but that is only one film, not half of the series. There is strong evidence that Wolverine is apocryphal because even before First Class, continuity problems ran amok through that film. With First Class rebooting Emma Frost's character and the upcoming Deadpool movie rebooting Wade Wilson, it looks pretty apparent that Wolverine is the bastard child of the series, but you have no proof that X3 has been retconned out other than your own hopes and dreams.
I agree that
First Class is clearly not a reboot in any way, shape or form for the series, and is not tossing aside
X-Men: The Last Stand continuity. As far as
X-Men Origins: Wolverine, I don't see that being tosses aside either. The same "contradiction" of
X-Men: The Last Stand is the same as the contradiction in
X-Men Origins: Wolverine - Xavier can walk.
As far as Emma Frost goes, well Emma is *never* referred to as Emma Frost in that movie. Only promo materials called her Emma Frost. Not the film itself. It can be seen in much the same way that the film's version of Victor Creed is not the same character as
X-Men's Sabretooth.
And I feel you're 100% right about Beast and Mystique. Beast's character arc matches up way too perfectly in
X-Men: First Class and
X-Men: The Last Stand, and Mystique being as youthful as she is after being cured is explained pretty well in
X-Men: First Class when Hank talks about her genetic makeup.
Until a sequel to
First Class comes out and establishes otherwise in official continuity, this is how I'm treating the timeframe between
X-Men: First Class and the rest of the films:
->
X-Men: First Class to
X-Men Origins: Wolverine - Havok learns about the disappearance of his brother, and upon informing Xavier, Xavier uses Cerebro to track Scott down. Xavier being able to walk, I accept as an inconsistency that isn't a significant alteration in the narrative.
->
X-Men: First Class to
X-Men: Xavier and Magneto are not "enemies" at the end of
First Class, merely a difference in ideology forces them to split and seek their own methods of achieving their goals. Magneto considers Xavier a friend, and still keeps a relationship with him, and even aids him in building a new version of Cerebro. With new mutants now at the school (Cyclops, Storm, Jean Grey...) Beast decides that he now wants to fight for mutant rights in a new way, and enters the political realm.
->
X-Men: First Class to
X2: Beast's cameo appearance is representative of Beast's venture into the political world. Beast being in human form, I accept as an inconsistency, no worse than re-casting of Kitty Pryde 3 times, or Pyro twice, or Storm's disappearing accent. The cameo is of no significance to the narrative.
->
X-Men: First Class to
X-Men: The Last Stand: Xavier learns about the existence of Jean Grey, the most powerful mutant he's ever encountered. The discovery of Jean Grey is a moment that brings Magneto and Xavier together, and they go together to recruit her, but the eventual treatment of Jean Grey at the hands of Xavier are the final falling out between Xavier and Magneto. Magneto goes his way, Xavier goes his, and the events of the trilogy occur. Xavier's ability to walk I accept as an inconsistency that doesn't have a significant impact on the narrative. Beast is a direct continuation of the version from
X-Men: First Class, Mystique's youthful appearance is addressed.
That is my take, until another film comes out that establishes otherwise. The inconsistencies caused by
X-Men: First Class with the other movies are of no significance towards the narrative, and the gaps between events can easily be filled in.