I'd probably treat it like a vintage graphic novel similiar to Watchmen, but not too overly dark and gritty in tone. But still heavily stylized. Not sure if it would haveto be canon to the established Xmen films, timeline wise, but I guess that would make sense.
So let's say if the film was set in the late 80s, early 90s. the X-Men universe could possibly exist in our history like with Bush Sr becoming president, the collapse of the Berlin Wall, End of the Cold War, possibly The Gulf War taking place that sort of thing. Coinciding with all this are mutants becoming more and more known to the public and somewhere in upstate New York, Professor X is building a school for the gifted and meanwhile Erik Lanshere, a former German officer/Hannibal Lecter type (sans the cannibalism) is being released from prison for war crimes, I dunno I guess WWII would make him too old so let's say for something he did in the Vietnam War, why a german officer is in Vietnam I have no idea, but anyways let's move on. I guess at this point he isn't Magneto yet, for all intent of purposes of this film, they could spinoff with a prequel of this as originally planned, but whatever. He allies himself with a group of evil mutants, but to switch things up from original roster of the Brotherhood, introduce new bad guys that haven't been onscreen yet, like Mr. sinister or maybe instead of the Brotherhood of Evil Mutants we go into a different direction entirely and maybe introduce The Hellfire Club? And have Sebastion Shaw be the antagonist, setting up an introduction for Magneto later on or even the Sentinels.
Back to the X-Men, I'd just use the original core team: Scott Summers, Jean Grey, Warren Worthing III, Bobby Drake and Dr. Henry McCoy and possibly supporting characters like Alex Summers, Ororo Munroe, and Emma Frost if we're dealing with the Hellfire Club,
Gonna have to get back to you guys on the casting though and that's all I got so far, but if they could not make Ice Man look like a walking Snow man who throws snow balls that be great. I'd also ditch the original FX team and hire ILM or WETA Studios for this, what you guys think so far?