The problem, from my perspective...and it's just MHO...is that Storm isn't 'anti' enough for them. They want anti-heroes for the X-Men line...that's why they've been killing off their 'moral paragon' characters since 2004 or so, when they haven't been tarnishing them with retcons or sudden personality changes.
Let's look at the roster of characters who are generally considered the X-Men's 'goody two shoes':
Cyclops - His story pretty much tells itself. Though I admit, most people actually like him better the way he is now. ('most' meaning 'not me', but I digress)
Nightcrawler - Has been made to look preachy and then was killed off after Pixie took a power-upgrade to be his replacement.
Beast - Has been made to look preachy, and got preachier as time went on until it became his sole defining character trait: the preachy guy.
Banshee - Squished between two planes.
Professor X - Had his good name smeared to the point where he's unrecognizable, sidelined into near-total irrelevancy, and then killed in a cheap, enigmatic fashion at the end of AvX.
Colossus - y helo thar Cytorrak.
Jean - 'jgg' Do I really need to say more? (Also, NO! I'M NOT OVER IT!)
The only heroes on the X-Men who aren't 'anti' right now are Kitty Pryde and Storm. And Kitty's been all-but completely sidelined off the team by her new duties as the the actual headmistress of Jean Grey School...you know, the person who does all the work?
So Marvel's caught in an awkward position. It's pretty clear they want to off or darken all their 'paragon' characters because Good Is Old-Fashioned, but killing Storm or derailing her too badly would cause a huge backlash, since she is pretty much the biggest non-white X-Man they've got. Hell, I'd argue she's the biggest female superhero they've got, regardless of how they've tried to sideline her to push others.