I had trouble caring about the events of Whedon's run, Morrison takes the basic concepts of the X-men, and makes them relevant to the 21st century. He was really the first to consider the idea that young mutants might be bored with the Xavier/Magneto debate, what a mutant school and mutant subculture might look like. The whole thing builds upon itself, and considers the ramifications of the events taking place. 139 might be the single best issue ever written regarding Emma Frost. Some arcs are better than others, and some people aren't entirely happy with his depiction of Magneto (myself included). Still he tells a self contained story that carries a degree of relevance within its own universe, which is more than I can say for most mainstream comics. Whedon's run tried to maintain the characters and relationships that Morrison had built, but it lacks the sense of eventful consequence that Morrison had, and I always found Ord to be a lame and uninteresting antagonist.
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