Sadly, the warped mind of Grant Morrison thought the x-books needed a shock to the system and created a mutant genocide to sell his new brand of storytelling at Marvel and change the status quo of the X-men.
I don't agree with that entirely. For all his faults, Morrison did far more to create the sense of an actual mutant culture than any writer who came before. For a brief, shining period (Morrison's run right up until Decimation) the X-Men really seemed to fit into the Marvel Universe because they fully grew into their niche, and a lot of that was because of Morrison.