Cyclops is about to catch a plane to Dallas, hoping to catch Freedom Force there to interview them about his wife (see, he really is allergic to telephones), but notices the news coverage about the Ship going wrong and returns to set things straight. They discover the Ship is actually sentient (although Apocalypse had blocked its higher-level functioning), and are left happier.
So. Our new premise for X-Factor is set up. What Bob Layton and Jackson Guice took one issue to construct has taken Louise Simonson two years and 23 issues to carefully demolish and replace with something more feasible. Plonking the Ship on top of the X-Factor headquarters was symbolic of this. But she's not just done it casually by trashing the status quo and letting the house of cards that the series was based on collapse; instead she's tried to find explanations for the things that never made sense, and then let the situation degenerate from there.
She's worked with the material that was there: we always knew that Hodge was a bad one, but during the Layton run I never got the sense that his plan was as big as we eventually saw. Similarly, the problem of Angel and secret identities was made out to have been plausible all along, but still a flaw in their plan. I like this fixing without repudiating. You wouldn't, as Teebore points out, get that today, someone would just come along and retcon it in a single issue.
In terms of characterisation we've moved on a lot too. I don't like what's being done with Scott and Madelyne here: I think it's being based on what Simonson and Claremont would have liked to have happened in X-Factor #1 rather than the text (the idea is drilled into us that she left him, which is simply not true, but it's repeated so often that I think they're just asking us to believe this new, more acceptable version of events rather than a 2-year-old back issue.) But what has been done to Warren is clearly an indication of a series not afraid to allow development. There's also Beast, who is suffering after-effects from the battle with the Horsemen and now has a Flowers for Algernon-style degeneration whenever he uses his strength.
In summary, this is a series that has redeemed itself, whose existence is now completely justified. It is not the worthless nostalgia fest that it started as, but something that can be used as a basis for telling completely different stories, that Uncanny X-Men has never been able to tell.