Onslaught will appear during the shows run.Hey, Age Of Apocalypse made an appearance, so, why not?
Gambit will join the team in Season 2.
Emma Frost is not dead.
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.
The Legacy Virus will be a future plot line, perhaps subplot.
This is the same universe Nocturne from Exiles originated from.
Stryfe would have appearred in Season 2.
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.
Cyclops would have finally done something heroic on his own with no help from anyone
Cyclops would finally figure out that Jean Grey was the wrong girlfriend for him, break up with her and go hook up with the resurrected Emma Frost, who obviously is right or at least a better girlfriend for him than Jean
The other X-Men besides Nightcrawler would finally get some actual character development.
Colossus and Kitty would finally get together