Wolverine and the X-Men/WMG

Onslaught will appear during the shows run.
Hey, Age Of Apocalypse made an appearance, so, why not?
 * Maybe because Xavier's in a coma for the next 20 years? So even if Onsluaght does pop up somewhere, it'd have to be in the Age Of Apocalypse...and an epic battle would ensue.
 * Perhaps he'd come to life because of the coma? While Xavier's unconscious, sooner or later, Onslaught will take control, hypothetically.

Gambit will join the team in Season 2.

 * Because the fans will want it.

Emma Frost is

 * Death Is Cheap in comics, even many of their adaptations.

Rogue is Logan and Mystique's daughter.
Back when he knew he was James Howlett, he and Raven got along much better than he currently knows. Sabretooth got jealous and ratted them out to Thorton and Cornelius, but Raven was already pregnant. She went into hiding to protect little Anna, and trusted her good friend Irene (Destiny) to raise her while she worked for Magneto to make the world a better place for mutants, including her and James'/Logan's daughter.
 * Logan fought in just about every major war, wars that Rouge never read about in history class.
 * He's originally british.

The Legacy Virus will be a future plot line, perhaps subplot.

 * It got a shout out with the 'legacy cure'. Perhaps the cure will be taken by a group of terrorists and corrupted into the virus, meant to kill mutants rather then cure them?

This is the same universe Nocturne from Exiles originated from.

 * Wanda and Nightcrawler in love? Check. Wolverine leader of the X-Men? Check. Cyclops Darker and Edgier? Check. The ground work is there. Hopefully she will at least appear in one of Xavier's futures.

Stryfe would have appearred in Season 2.

 * Sinister had Scott's and Jean's DNA, and I doubt he'd be eager to make Cable or X-Man.
 * He's been eager to make them before, he just didn't expect the results he got.

Future!Xavier is suffering from dementia.
Possibly caused by or compounded by the brain damage from his long coma. That's why he picked loner Wolverine as leader instead of groomed-for-leadership-since-puberty Cyclops.

The whole series is a Danger Room scenario to test whether Wolverine is any good at leadership.

 * Judging by the show's cancellation, he failed.